绝对结合自由能是蛋白质-小分子动力学模拟中非常重要的一部分内容，与相对结合自由能如FEP相比，它更适合相对更加上游的药物发现阶段，即小分子的相似性还不足以足够大到能够进行相对结合自由能得计算时。但与FEP等相对结合自由能得计算现装类似，其计算过程繁杂，对操作者要求较高，步骤很多，且需要较高得计算机算力，这些都严重制约了其应用范围，而付费软件价格十分昂贵，暂时无法大规模普及。 这个脚本是我专门针对谷歌免费得计算平台colab 而写，整合了现存得基于Gromacs得两大教程，即Justin 得protein complex 教程和 AlchemistryWiki 上得绝对结合自由能教程而来。原先得两个教程都是针对已经安装了Gromacs得本地计算机，第二个绝对结合自由能教程更是默认使用者拥有较好的算力资源。而这个脚本力求减少操作者得手动操作步骤，使得初级得分子模拟者也有机会真正使用网络上免费的算力来进行绝对结合自由能这个方法，以应用在他们各自得科研或者商业研发活动中，可极大降低使用成本，使得对蛋白质-小分子亲和力的计算不完全局限于分子对接等模拟技术。
我完全修改了原脚本中空着整体运算进度的run.sh，使用一个简单明了基于两个变量a,b的for 循环语句，以便使得使用者可以通过自行修改a.b来控制自由能计算的时间不超出colab 的12 小时上限。但需要强调的是，这个脚本正在不断的完善中，因此，目前，还是有不少的步骤需要操作者去主动参与和干预。你可先使用蛋白质3htb 走一遍整个流程，再应用到你自己的蛋白-小分子体系中去。如果你有问题或者好的修改建议请邮件 quantaosun@gmail.com
Absolute binding free engergy calculation by Gromacs 2021 GPU. Compilation and Calculations on Google Colab.
Created by Quantao 知乎账号 奋进的涛 https://www.zhihu.com/people/qutesun
This template can be divided into two parts, the fisrt part is the same as Justin's tutorial of protein ligand simulation http://www.mdtutorials.com/gmx/complex/, the second part is my modification inspired by http://www.alchemistry.org/wiki/Absolute_Binding_Free_Energy_-_Gromacs_2016 Note,for the second part, many running commands and overall FEP folder structures have been changed significantly to make it suitable for colab, like the for loop inside run.sh and name style of lambda folders. etc.
Credit to the work of giribio/MDNotebooks as well, since the software compilation method is borrowed there.
If you find installing or running gromacs on online platform is not your preference, you could just use half of this notebook to prepare the ABFE input, then copy the input files to your prefered platform, the only thing to keep in mind is that you need to make sure to use the SAME version of Gromacs across different platforms!
Someone else might prefer to do it the other way round, so you could just prepare your ABFE in your laptop as per the procedures in this notebook and then upload the input files to run the job on colab or AI studio for people in China.
Limitations: Every 12hrs the data gets reset, so in free account you could use it for training/learning purpose only.
Every 12hrs you have to start from 1st cell, like compilation etc.
And beware if you leave the window for a long time without any editing (like 1 hour), the runtime may also
broke out, then you have to start over again.You need to switch to GPU when you do the simulation to speed up the process.¶
In [ ]:
In [ ]:
#Let us check the Google COlab resources - 1GPU and 2 CPU with 1TB HDD and 12GB RAM
%%bash
lscpu
nvidia-smi
Architecture: x86_64
CPU op-mode(s): 32-bit, 64-bit
Byte Order: Little Endian
CPU(s): 2
On-line CPU(s) list: 0,1
Thread(s) per core: 2
Core(s) per socket: 1
Socket(s): 1
NUMA node(s): 1
Vendor ID: GenuineIntel
CPU family: 6
Model: 79
Model name: Intel(R) Xeon(R) CPU @ 2.20GHz
Stepping: 0
CPU MHz: 2199.998
BogoMIPS: 4399.99
Hypervisor vendor: KVM
Virtualization type: full
L1d cache: 32K
L1i cache: 32K
L2 cache: 256K
L3 cache: 56320K
NUMA node0 CPU(s): 0,1
Flags: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ss ht syscall nx pdpe1gb rdtscp lm constant_tsc rep_good nopl xtopology nonstop_tsc cpuid tsc_known_freq pni pclmulqdq ssse3 fma cx16 pcid sse4_1 sse4_2 x2apic movbe popcnt aes xsave avx f16c rdrand hypervisor lahf_lm abm 3dnowprefetch invpcid_single ssbd ibrs ibpb stibp fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm rdseed adx smap xsaveopt arat md_clear arch_capabilities
Thu Jun 10 06:10:19 2021
+-----------------------------------------------------------------------------+
| NVIDIA-SMI 465.27 Driver Version: 460.32.03 CUDA Version: 11.2 |
|-------------------------------+----------------------+----------------------+
| GPU Name Persistence-M| Bus-Id Disp.A | Volatile Uncorr. ECC |
| Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. |
| | | MIG M. |
|===============================+======================+======================|
| 0 Tesla T4 Off | 00000000:00:04.0 Off | 0 |
| N/A 51C P8 10W / 70W | 0MiB / 15109MiB | 0% Default |
| | | N/A |
+-------------------------------+----------------------+----------------------+
+-----------------------------------------------------------------------------+
| Processes: |
| GPU GI CI PID Type Process name GPU Memory |
| ID ID Usage |
|=============================================================================|
| No running processes found |
+-----------------------------------------------------------------------------+
Let's install a tool to get access to the ABFE input files from google drive¶
In [ ]:
!pip install PyDrive
Requirement already satisfied: PyDrive in /usr/local/lib/python3.7/dist-packages (1.3.1) Requirement already satisfied: PyYAML>=3.0 in /usr/local/lib/python3.7/dist-packages (from PyDrive) (3.13) Requirement already satisfied: oauth2client>=4.0.0 in /usr/local/lib/python3.7/dist-packages (from PyDrive) (4.1.3) Requirement already satisfied: google-api-python-client>=1.2 in /usr/local/lib/python3.7/dist-packages (from PyDrive) (1.12.8) Requirement already satisfied: httplib2>=0.9.1 in /usr/local/lib/python3.7/dist-packages (from oauth2client>=4.0.0->PyDrive) (0.17.4) Requirement already satisfied: pyasn1>=0.1.7 in /usr/local/lib/python3.7/dist-packages (from oauth2client>=4.0.0->PyDrive) (0.4.8) Requirement already satisfied: pyasn1-modules>=0.0.5 in /usr/local/lib/python3.7/dist-packages (from oauth2client>=4.0.0->PyDrive) (0.2.8) Requirement already satisfied: six>=1.6.1 in /usr/local/lib/python3.7/dist-packages (from oauth2client>=4.0.0->PyDrive) (1.15.0) Requirement already satisfied: rsa>=3.1.4 in /usr/local/lib/python3.7/dist-packages (from oauth2client>=4.0.0->PyDrive) (4.7.2) Requirement already satisfied: google-auth-httplib2>=0.0.3 in /usr/local/lib/python3.7/dist-packages (from google-api-python-client>=1.2->PyDrive) (0.0.4) Requirement already satisfied: google-api-core<2dev,>=1.21.0 in /usr/local/lib/python3.7/dist-packages (from google-api-python-client>=1.2->PyDrive) (1.26.3) Requirement already satisfied: google-auth>=1.16.0 in /usr/local/lib/python3.7/dist-packages (from google-api-python-client>=1.2->PyDrive) (1.30.0) Requirement already satisfied: uritemplate<4dev,>=3.0.0 in /usr/local/lib/python3.7/dist-packages (from google-api-python-client>=1.2->PyDrive) (3.0.1) Requirement already satisfied: pytz in /usr/local/lib/python3.7/dist-packages (from google-api-core<2dev,>=1.21.0->google-api-python-client>=1.2->PyDrive) (2018.9) Requirement already satisfied: googleapis-common-protos<2.0dev,>=1.6.0 in /usr/local/lib/python3.7/dist-packages (from google-api-core<2dev,>=1.21.0->google-api-python-client>=1.2->PyDrive) (1.53.0) Requirement already satisfied: packaging>=14.3 in /usr/local/lib/python3.7/dist-packages (from google-api-core<2dev,>=1.21.0->google-api-python-client>=1.2->PyDrive) (20.9) Requirement already satisfied: setuptools>=40.3.0 in /usr/local/lib/python3.7/dist-packages (from google-api-core<2dev,>=1.21.0->google-api-python-client>=1.2->PyDrive) (57.0.0) Requirement already satisfied: requests<3.0.0dev,>=2.18.0 in /usr/local/lib/python3.7/dist-packages (from google-api-core<2dev,>=1.21.0->google-api-python-client>=1.2->PyDrive) (2.23.0) Requirement already satisfied: protobuf>=3.12.0 in /usr/local/lib/python3.7/dist-packages (from google-api-core<2dev,>=1.21.0->google-api-python-client>=1.2->PyDrive) (3.12.4) Requirement already satisfied: cachetools<5.0,>=2.0.0 in /usr/local/lib/python3.7/dist-packages (from google-auth>=1.16.0->google-api-python-client>=1.2->PyDrive) (4.2.2) Requirement already satisfied: pyparsing>=2.0.2 in /usr/local/lib/python3.7/dist-packages (from packaging>=14.3->google-api-core<2dev,>=1.21.0->google-api-python-client>=1.2->PyDrive) (2.4.7) Requirement already satisfied: chardet<4,>=3.0.2 in /usr/local/lib/python3.7/dist-packages (from requests<3.0.0dev,>=2.18.0->google-api-core<2dev,>=1.21.0->google-api-python-client>=1.2->PyDrive) (3.0.4) Requirement already satisfied: idna<3,>=2.5 in /usr/local/lib/python3.7/dist-packages (from requests<3.0.0dev,>=2.18.0->google-api-core<2dev,>=1.21.0->google-api-python-client>=1.2->PyDrive) (2.10) Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /usr/local/lib/python3.7/dist-packages (from requests<3.0.0dev,>=2.18.0->google-api-core<2dev,>=1.21.0->google-api-python-client>=1.2->PyDrive) (1.24.3) Requirement already satisfied: certifi>=2017.4.17 in /usr/local/lib/python3.7/dist-packages (from requests<3.0.0dev,>=2.18.0->google-api-core<2dev,>=1.21.0->google-api-python-client>=1.2->PyDrive) (2020.12.5)
In [ ]:
from pydrive.auth import GoogleAuth
from pydrive.drive import GoogleDrive
from google.colab import auth
from oauth2client.client import GoogleCredentials
In [ ]:
auth.authenticate_user()
gauth = GoogleAuth()
gauth.credentials = GoogleCredentials.get_application_default()
drive = GoogleDrive(gauth)
In [ ]:
downloaded = drive.CreateFile({'id':"1hvA1zsA3cwQaVNaqPBj9Ol6IjwhXDCoM"}) # replace the id with id of file you want to access https://drive.google.com/file/d/1hvA1zsA3cwQaVNaqPBj9Ol6IjwhXDCoM/view?usp=sharing
downloaded.GetContentFile('ABFE_input_files.tar.gz')
In [ ]:
!tar -xzvf ABFE_input_files.tar.gz
new/ new/complex/ new/complex/lambda.1.7/ new/complex/lambda.0.1/ new/complex/lambda.0.1/ENMIN/ new/complex/lambda.0.1/ENMIN/mdout.mdp new/complex/lambda.0.1/NPT/ new/complex/lambda.0.1/NVT/ new/complex/lambda.0.1/PROD/ new/complex/lambda.2.6/ new/complex/jz4.prm new/complex/jz4.itp new/complex/lambda.2.4/ new/complex/posre_jz4.itp new/complex/lambda.1.9/ new/complex/index_jz4.ndx new/complex/posre.itp new/complex/lambda.1.1/ new/complex/lambda.1.5/ new/complex/lambda.0.7/ new/complex/lambda.0.6/ new/complex/lambda.0.5/ new/complex/lambda.2.2/ new/complex/lambda.2.9/ new/complex/lambda.1.8/ new/complex/lambda.2.3/ new/complex/00_03_run.sh new/complex/jz4.gro new/complex/lambda.0.2/ new/complex/lambda.0.2/ENMIN/ new/complex/lambda.0.2/ENMIN/mdout.mdp new/complex/lambda.0.2/NPT/ new/complex/lambda.0.2/NVT/ new/complex/lambda.0.2/PROD/ new/complex/lambda.1.3/ new/complex/MDP/ new/complex/MDP/ENMIN/ new/complex/MDP/ENMIN/enmin.1.0.mdp new/complex/MDP/ENMIN/enmin.2.6.mdp new/complex/MDP/ENMIN/enmin.1.1.mdp new/complex/MDP/ENMIN/enmin.1.3.mdp new/complex/MDP/ENMIN/enmin.2.1.mdp new/complex/MDP/ENMIN/enmin.1.4.mdp new/complex/MDP/ENMIN/enmin.0.0.mdp new/complex/MDP/ENMIN/enmin.2.0.mdp new/complex/MDP/ENMIN/enmin.2.9.mdp new/complex/MDP/ENMIN/enmin.0.1.mdp new/complex/MDP/ENMIN/enmin.1.5.mdp new/complex/MDP/ENMIN/enmin.1.8.mdp new/complex/MDP/ENMIN/enmin.1.2.mdp new/complex/MDP/ENMIN/enmin.0.5.mdp new/complex/MDP/ENMIN/enmin.2.7.mdp new/complex/MDP/ENMIN/enmin.0.7.mdp new/complex/MDP/ENMIN/enmin.2.2.mdp new/complex/MDP/ENMIN/enmin.1.9.mdp new/complex/MDP/ENMIN/enmin.0.2.mdp new/complex/MDP/ENMIN/enmin.0.9.mdp new/complex/MDP/ENMIN/enmin.0.8.mdp new/complex/MDP/ENMIN/enmin.2.3.mdp new/complex/MDP/ENMIN/enmin.2.4.mdp new/complex/MDP/ENMIN/enmin.1.6.mdp new/complex/MDP/ENMIN/enmin.0.6.mdp new/complex/MDP/ENMIN/enmin.1.7.mdp new/complex/MDP/ENMIN/enmin.2.5.mdp new/complex/MDP/ENMIN/enmin.2.8.mdp new/complex/MDP/ENMIN/enmin.0.4.mdp new/complex/MDP/ENMIN/enmin.0.3.mdp new/complex/MDP/NPT/ new/complex/MDP/NPT/npt.2.5.mdp new/complex/MDP/NPT/npt.1.6.mdp new/complex/MDP/NPT/npt.0.7.mdp new/complex/MDP/NPT/npt.0.6.mdp new/complex/MDP/NPT/npt.0.5.mdp new/complex/MDP/NPT/npt.0.1.mdp new/complex/MDP/NPT/npt.1.5.mdp new/complex/MDP/NPT/npt.0.9.mdp new/complex/MDP/NPT/npt.1.4.mdp new/complex/MDP/NPT/npt.0.3.mdp new/complex/MDP/NPT/npt.1.1.mdp new/complex/MDP/NPT/npt.1.0.mdp new/complex/MDP/NPT/npt.1.8.mdp new/complex/MDP/NPT/npt.2.1.mdp new/complex/MDP/NPT/npt.1.7.mdp new/complex/MDP/NPT/npt.2.3.mdp new/complex/MDP/NPT/npt.1.2.mdp new/complex/MDP/NPT/npt.2.0.mdp new/complex/MDP/NPT/npt.1.3.mdp new/complex/MDP/NPT/npt.0.0.mdp new/complex/MDP/NPT/npt.2.6.mdp new/complex/MDP/NPT/npt.2.7.mdp new/complex/MDP/NPT/npt.1.9.mdp new/complex/MDP/NPT/npt.2.8.mdp new/complex/MDP/NPT/npt.2.2.mdp new/complex/MDP/NPT/npt.2.4.mdp new/complex/MDP/NPT/npt.0.4.mdp new/complex/MDP/NPT/npt.0.8.mdp new/complex/MDP/NPT/npt.2.9.mdp new/complex/MDP/NPT/npt.0.2.mdp new/complex/MDP/NVT/ new/complex/MDP/NVT/nvt.2.3.mdp new/complex/MDP/NVT/nvt.1.7.mdp new/complex/MDP/NVT/nvt.0.7.mdp new/complex/MDP/NVT/nvt.1.5.mdp new/complex/MDP/NVT/nvt.1.3.mdp new/complex/MDP/NVT/nvt.0.1.mdp new/complex/MDP/NVT/nvt.0.2.mdp new/complex/MDP/NVT/nvt.2.1.mdp new/complex/MDP/NVT/nvt.1.6.mdp new/complex/MDP/NVT/nvt.1.4.mdp new/complex/MDP/NVT/nvt.2.2.mdp new/complex/MDP/NVT/nvt.0.6.mdp new/complex/MDP/NVT/nvt.0.8.mdp new/complex/MDP/NVT/nvt.2.5.mdp new/complex/MDP/NVT/nvt.2.0.mdp new/complex/MDP/NVT/nvt.0.0.mdp new/complex/MDP/NVT/nvt.2.7.mdp new/complex/MDP/NVT/nvt.1.0.mdp new/complex/MDP/NVT/nvt.1.1.mdp new/complex/MDP/NVT/nvt.0.9.mdp new/complex/MDP/NVT/nvt.2.9.mdp new/complex/MDP/NVT/nvt.1.2.mdp new/complex/MDP/NVT/nvt.0.4.mdp new/complex/MDP/NVT/nvt.1.8.mdp new/complex/MDP/NVT/nvt.2.6.mdp new/complex/MDP/NVT/nvt.0.3.mdp new/complex/MDP/NVT/nvt.2.4.mdp new/complex/MDP/NVT/nvt.2.8.mdp new/complex/MDP/NVT/nvt.1.9.mdp new/complex/MDP/NVT/nvt.0.5.mdp new/complex/MDP/PROD/ new/complex/MDP/PROD/prod.0.1.mdp new/complex/MDP/PROD/prod.2.2.mdp new/complex/MDP/PROD/prod.0.0.mdp new/complex/MDP/PROD/prod.2.1.mdp new/complex/MDP/PROD/prod.0.3.mdp new/complex/MDP/PROD/prod.1.0.mdp new/complex/MDP/PROD/prod.1.4.mdp new/complex/MDP/PROD/prod.2.0.mdp new/complex/MDP/PROD/prod.1.3.mdp new/complex/MDP/PROD/prod.1.9.mdp new/complex/MDP/PROD/prod.2.4.mdp new/complex/MDP/PROD/prod.0.7.mdp new/complex/MDP/PROD/prod.0.4.mdp new/complex/MDP/PROD/prod.1.1.mdp new/complex/MDP/PROD/prod.0.5.mdp new/complex/MDP/PROD/prod.1.7.mdp new/complex/MDP/PROD/prod.0.9.mdp new/complex/MDP/PROD/prod.0.6.mdp new/complex/MDP/PROD/prod.1.6.mdp new/complex/MDP/PROD/prod.2.9.mdp new/complex/MDP/PROD/prod.2.3.mdp new/complex/MDP/PROD/prod.0.8.mdp new/complex/MDP/PROD/prod.2.7.mdp new/complex/MDP/PROD/prod.2.6.mdp new/complex/MDP/PROD/prod.2.8.mdp new/complex/MDP/PROD/prod.1.5.mdp new/complex/MDP/PROD/prod.0.2.mdp new/complex/MDP/PROD/prod.1.2.mdp new/complex/MDP/PROD/prod.2.5.mdp new/complex/MDP/PROD/prod.1.8.mdp new/complex/MDP/mk_mdp.sh new/complex/MDP/.DS_Store new/complex/lambda.1.6/ new/complex/lambda.2.7/ new/complex/lambda.0.8/ new/complex/lambda.2.1/ new/complex/lambda.0.3/ new/complex/charmm36-mar2019.ff/ new/complex/charmm36-mar2019.ff/merged.n.tdb new/complex/charmm36-mar2019.ff/merged.c.tdb new/complex/charmm36-mar2019.ff/spce.itp new/complex/charmm36-mar2019.ff/forcefield.doc new/complex/charmm36-mar2019.ff/merged.rtp new/complex/charmm36-mar2019.ff/watermodels.dat new/complex/charmm36-mar2019.ff/merged.hdb new/complex/charmm36-mar2019.ff/tip4p.itp new/complex/charmm36-mar2019.ff/ions.itp new/complex/charmm36-mar2019.ff/atomtypes.atp new/complex/charmm36-mar2019.ff/spc.itp new/complex/charmm36-mar2019.ff/tip3p.itp new/complex/charmm36-mar2019.ff/nbfix.itp new/complex/charmm36-mar2019.ff/ffnonbonded.itp new/complex/charmm36-mar2019.ff/merged.arn new/complex/charmm36-mar2019.ff/forcefield.itp new/complex/charmm36-mar2019.ff/merged.r2b new/complex/charmm36-mar2019.ff/old_c36_cmap.itp new/complex/charmm36-mar2019.ff/merged.vsd new/complex/charmm36-mar2019.ff/gb.itp new/complex/charmm36-mar2019.ff/cmap.itp new/complex/charmm36-mar2019.ff/ffbonded.itp new/complex/index.ndx new/complex/jz4.top new/complex/lambda.1.2/ new/complex/lambda.0.9/ new/complex/topol.top new/complex/lambda.0.4/ new/complex/lambda.2.0/ new/complex/lambda.1.4/ new/complex/solv_ions.gro new/complex/lambda.1.0/ new/complex/lambda.2.5/ new/complex/lambda.2.8/ new/complex/lambda.0.0/ new/complex/lambda.0.0/ENMIN/ new/complex/lambda.0.0/ENMIN/#enmin.trr.1# new/complex/lambda.0.0/ENMIN/#enmin.gro.1# new/complex/lambda.0.0/ENMIN/#enmin.tpr.1# new/complex/lambda.0.0/ENMIN/enmin.log new/complex/lambda.0.0/ENMIN/#enmin.log.1# new/complex/lambda.0.0/ENMIN/enmin.gro new/complex/lambda.0.0/ENMIN/enmin.tpr new/complex/lambda.0.0/ENMIN/mdout.mdp new/complex/lambda.0.0/ENMIN/#enmin.edr.1# new/complex/lambda.0.0/ENMIN/enmin.edr new/complex/lambda.0.0/ENMIN/enmin.trr new/complex/lambda.0.0/NPT/ new/complex/lambda.0.0/NPT/npt.gro new/complex/lambda.0.0/NPT/#npt.log.1# new/complex/lambda.0.0/NPT/npt.tpr new/complex/lambda.0.0/NPT/npt.edr new/complex/lambda.0.0/NPT/#npt.edr.1# new/complex/lambda.0.0/NPT/npt.cpt new/complex/lambda.0.0/NPT/npt.xtc new/complex/lambda.0.0/NPT/#npt.tpr.1# new/complex/lambda.0.0/NPT/npt.log new/complex/lambda.0.0/NPT/#npt.xtc.1# new/complex/lambda.0.0/NPT/npt.xvg new/complex/lambda.0.0/NPT/mdout.mdp new/complex/lambda.0.0/NPT/#npt.xvg.1# new/complex/lambda.0.0/NVT/ new/complex/lambda.0.0/NVT/#nvt.tpr.1# new/complex/lambda.0.0/NVT/#nvt.xtc.1# new/complex/lambda.0.0/NVT/nvt_prev.cpt new/complex/lambda.0.0/NVT/#nvt.gro.1# new/complex/lambda.0.0/NVT/#nvt.log.1# new/complex/lambda.0.0/NVT/nvt.xvg new/complex/lambda.0.0/NVT/nvt.xtc new/complex/lambda.0.0/NVT/#nvt.edr.1# new/complex/lambda.0.0/NVT/nvt.log new/complex/lambda.0.0/NVT/nvt.cpt new/complex/lambda.0.0/NVT/mdout.mdp new/complex/lambda.0.0/NVT/nvt.tpr new/complex/lambda.0.0/NVT/nvt.gro new/complex/lambda.0.0/NVT/#nvt.xvg.1# new/complex/lambda.0.0/NVT/nvt.edr new/complex/lambda.0.0/PROD/ new/complex/lambda.0.0/PROD/ENMIN/ new/complex/lambda.0.0/PROD/NPT/ new/complex/lambda.0.0/PROD/prod.tpr new/complex/lambda.0.0/PROD/NVT/ new/complex/lambda.0.0/PROD/PROD/ new/complex/lambda.0.0/PROD/PROD/ENMIN/ new/complex/lambda.0.0/PROD/PROD/NPT/ new/complex/lambda.0.0/PROD/PROD/NVT/ new/complex/lambda.0.0/PROD/PROD/PROD/ new/complex/lambda.0.0/PROD/mdout.mdp new/solvent/ new/solvent/lambda.1.7/ new/solvent/lambda.0.1/ new/solvent/jz4.prm new/solvent/jz4.itp new/solvent/posre_jz4.itp new/solvent/lambda.1.9/ new/solvent/index_jz4.ndx new/solvent/lambda.1.1/ new/solvent/lambda.1.5/ new/solvent/lambda.0.7/ new/solvent/lambda.0.6/ new/solvent/lambda.0.5/ new/solvent/lambda.1.8/ new/solvent/jz4.gro new/solvent/run.sh new/solvent/lambda.0.2/ new/solvent/lambda.1.3/ new/solvent/MDP/ new/solvent/MDP/ENMIN/ new/solvent/MDP/ENMIN/enmin.02.mdp new/solvent/MDP/ENMIN/enmin.16.mdp new/solvent/MDP/ENMIN/enmin.00.mdp new/solvent/MDP/ENMIN/enmin.05.mdp new/solvent/MDP/ENMIN/enmin.13.mdp new/solvent/MDP/ENMIN/enmin.10.mdp new/solvent/MDP/ENMIN/enmin.11.mdp new/solvent/MDP/ENMIN/enmin.14.mdp new/solvent/MDP/ENMIN/enmin.07.mdp new/solvent/MDP/ENMIN/enmin.01.mdp new/solvent/MDP/ENMIN/enmin.15.mdp new/solvent/MDP/ENMIN/enmin.18.mdp new/solvent/MDP/ENMIN/enmin.17.mdp new/solvent/MDP/ENMIN/enmin.03.mdp new/solvent/MDP/ENMIN/enmin.04.mdp new/solvent/MDP/ENMIN/enmin.19.mdp new/solvent/MDP/ENMIN/enmin.09.mdp new/solvent/MDP/ENMIN/enmin.12.mdp new/solvent/MDP/ENMIN/enmin.08.mdp new/solvent/MDP/ENMIN/enmin.06.mdp new/solvent/MDP/NPT/ new/solvent/MDP/NPT/npt.15.mdp new/solvent/MDP/NPT/npt.19.mdp new/solvent/MDP/NPT/npt.14.mdp new/solvent/MDP/NPT/npt.01.mdp new/solvent/MDP/NPT/npt.08.mdp new/solvent/MDP/NPT/npt.03.mdp new/solvent/MDP/NPT/npt.12.mdp new/solvent/MDP/NPT/npt.04.mdp new/solvent/MDP/NPT/npt.13.mdp new/solvent/MDP/NPT/npt.16.mdp new/solvent/MDP/NPT/npt.11.mdp new/solvent/MDP/NPT/npt.10.mdp new/solvent/MDP/NPT/npt.06.mdp new/solvent/MDP/NPT/npt.00.mdp new/solvent/MDP/NPT/npt.02.mdp new/solvent/MDP/NPT/npt.18.mdp new/solvent/MDP/NPT/npt.17.mdp new/solvent/MDP/NPT/npt.07.mdp new/solvent/MDP/NPT/npt.05.mdp new/solvent/MDP/NPT/npt.09.mdp new/solvent/MDP/NVT/ new/solvent/MDP/NVT/nvt.12.mdp new/solvent/MDP/NVT/nvt.13.mdp new/solvent/MDP/NVT/nvt.03.mdp new/solvent/MDP/NVT/nvt.16.mdp new/solvent/MDP/NVT/nvt.00.mdp new/solvent/MDP/NVT/nvt.07.mdp new/solvent/MDP/NVT/nvt.08.mdp new/solvent/MDP/NVT/nvt.01.mdp new/solvent/MDP/NVT/nvt.05.mdp new/solvent/MDP/NVT/nvt.06.mdp new/solvent/MDP/NVT/nvt.02.mdp new/solvent/MDP/NVT/nvt.14.mdp new/solvent/MDP/NVT/nvt.17.mdp new/solvent/MDP/NVT/nvt.11.mdp new/solvent/MDP/NVT/nvt.09.mdp new/solvent/MDP/NVT/nvt.19.mdp new/solvent/MDP/NVT/nvt.18.mdp new/solvent/MDP/NVT/nvt.15.mdp new/solvent/MDP/NVT/nvt.04.mdp new/solvent/MDP/NVT/nvt.10.mdp new/solvent/MDP/PROD/ new/solvent/MDP/PROD/prod.03.mdp new/solvent/MDP/PROD/prod.01.mdp new/solvent/MDP/PROD/prod.06.mdp new/solvent/MDP/PROD/prod.07.mdp new/solvent/MDP/PROD/prod.12.mdp new/solvent/MDP/PROD/prod.14.mdp new/solvent/MDP/PROD/prod.16.mdp new/solvent/MDP/PROD/prod.15.mdp new/solvent/MDP/PROD/prod.11.mdp new/solvent/MDP/PROD/prod.19.mdp new/solvent/MDP/PROD/prod.05.mdp new/solvent/MDP/PROD/prod.17.mdp new/solvent/MDP/PROD/prod.09.mdp new/solvent/MDP/PROD/prod.04.mdp new/solvent/MDP/PROD/prod.00.mdp new/solvent/MDP/PROD/prod.08.mdp new/solvent/MDP/PROD/prod.02.mdp new/solvent/MDP/PROD/prod.13.mdp new/solvent/MDP/PROD/prod.10.mdp new/solvent/MDP/PROD/prod.18.mdp new/solvent/MDP/.DS_Store new/solvent/lambda.1.6/ new/solvent/lambda.0.8/ new/solvent/lambda.0.3/ new/solvent/jz4.top new/solvent/lambda.1.2/ new/solvent/lambda.0.9/ new/solvent/lambda.0.4/ new/solvent/lambda.1.4/ new/solvent/lambda.1.0/ new/solvent/lambda.0.0/
Let us download the latest CMake - required for Gromacs 2021
In [ ]:
%%bash
wget https://github.com/Kitware/CMake/releases/download/v3.20.0-rc1/cmake-3.20.0-rc1.tar.gz
tar xfz cmake-3.20.0-rc1.tar.gz
--2021-06-10 06:14:02-- https://github.com/Kitware/CMake/releases/download/v3.20.0-rc1/cmake-3.20.0-rc1.tar.gz
Resolving github.com (github.com)... 192.30.255.113
Connecting to github.com (github.com)|192.30.255.113|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://github-releases.githubusercontent.com/537699/06e77180-705e-11eb-8500-bec51c1075dc?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20210610%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20210610T061402Z&X-Amz-Expires=300&X-Amz-Signature=68d37d0e57cfd17b53d2f766c484f9d7de47f6525375d4ec484e14782eb03e18&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=537699&response-content-disposition=attachment%3B%20filename%3Dcmake-3.20.0-rc1.tar.gz&response-content-type=application%2Foctet-stream [following]
--2021-06-10 06:14:02-- https://github-releases.githubusercontent.com/537699/06e77180-705e-11eb-8500-bec51c1075dc?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20210610%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20210610T061402Z&X-Amz-Expires=300&X-Amz-Signature=68d37d0e57cfd17b53d2f766c484f9d7de47f6525375d4ec484e14782eb03e18&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=537699&response-content-disposition=attachment%3B%20filename%3Dcmake-3.20.0-rc1.tar.gz&response-content-type=application%2Foctet-stream
Resolving github-releases.githubusercontent.com (github-releases.githubusercontent.com)... 185.199.108.154, 185.199.109.154, 185.199.110.154, ...
Connecting to github-releases.githubusercontent.com (github-releases.githubusercontent.com)|185.199.108.154|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 9425531 (9.0M) [application/octet-stream]
Saving to: ‘cmake-3.20.0-rc1.tar.gz’
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9200K .... 100% 138M=0.4s
2021-06-10 06:14:03 (20.6 MB/s) - ‘cmake-3.20.0-rc1.tar.gz’ saved [9425531/9425531]
Install cmake¶
In [ ]:
%%bash
mkdir /content/cmake-3.20.0-rc1/build
cd /content/cmake-3.20.0-rc1/build
cmake /content/cmake-3.20.0-rc1/
make -j 2
make install
-- Installing: /usr/local/share/bash-completion/completions/ctest
In [ ]:
%%bash
wget ftp://ftp.gromacs.org/gromacs/gromacs-2021.tar.gz
tar xfz gromacs-2021.tar.gz
cd /content/gromacs-2021
mkdir /content/gromacs-2021/build
cd /content/gromacs-2021/build
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=CUDA
make -j 2
make install
source /usr/local/gromacs/bin/GMXRC
-- Installing: /usr/local/gromacs/bin/gmx-completion-gmx.bash
--2021-06-10 06:30:38-- ftp://ftp.gromacs.org/gromacs/gromacs-2021.tar.gz
=> ‘gromacs-2021.tar.gz’
Resolving ftp.gromacs.org (ftp.gromacs.org)... 130.237.11.165, 2001:6b0:1:1191:216:3eff:fec7:6e30
Connecting to ftp.gromacs.org (ftp.gromacs.org)|130.237.11.165|:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done. ==> PWD ... done.
==> TYPE I ... done. ==> CWD (1) /gromacs ... done.
==> SIZE gromacs-2021.tar.gz ... 35061679
==> PASV ... done. ==> RETR gromacs-2021.tar.gz ... done.
Length: 35061679 (33M) (unauthoritative)
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12200K .......... .......... .......... .......... .......... 35% 7.89M 3s
12250K .......... .......... .......... .......... .......... 35% 17.4M 3s
12300K .......... .......... .......... .......... .......... 36% 13.8M 3s
12350K .......... .......... .......... .......... .......... 36% 82.7M 3s
12400K .......... .......... .......... .......... .......... 36% 11.0M 3s
12450K .......... .......... .......... .......... .......... 36% 10.6M 3s
12500K .......... .......... .......... .......... .......... 36% 9.50M 3s
12550K .......... .......... .......... .......... .......... 36% 11.6M 3s
12600K .......... .......... .......... .......... .......... 36% 22.8M 3s
12650K .......... .......... .......... .......... .......... 37% 13.3M 3s
12700K .......... .......... .......... .......... .......... 37% 23.4M 3s
12750K .......... .......... .......... .......... .......... 37% 12.4M 3s
12800K .......... .......... .......... .......... .......... 37% 21.1M 3s
12850K .......... .......... .......... .......... .......... 37% 10.7M 3s
12900K .......... .......... .......... .......... .......... 37% 44.2M 3s
12950K .......... .......... .......... .......... .......... 37% 11.9M 3s
13000K .......... .......... .......... .......... .......... 38% 11.3M 3s
13050K .......... .......... .......... .......... .......... 38% 29.3M 3s
13100K .......... .......... .......... .......... .......... 38% 12.7M 3s
13150K .......... .......... .......... .......... .......... 38% 24.3M 3s
13200K .......... .......... .......... .......... .......... 38% 8.60M 3s
13250K .......... .......... .......... .......... .......... 38% 26.1M 3s
13300K .......... .......... .......... .......... .......... 38% 248M 3s
13350K .......... .......... .......... .......... .......... 39% 15.4M 3s
13400K .......... .......... .......... .......... .......... 39% 14.1M 3s
13450K .......... .......... .......... .......... .......... 39% 20.8M 3s
13500K .......... .......... .......... .......... .......... 39% 77.3M 3s
13550K .......... .......... .......... .......... .......... 39% 8.59M 3s
13600K .......... .......... .......... .......... .......... 39% 16.6M 3s
13650K .......... .......... .......... .......... .......... 40% 13.2M 3s
13700K .......... .......... .......... .......... .......... 40% 34.5M 3s
13750K .......... .......... .......... .......... .......... 40% 105M 3s
13800K .......... .......... .......... .......... .......... 40% 18.4M 3s
13850K .......... .......... .......... .......... .......... 40% 13.1M 3s
13900K .......... .......... .......... .......... .......... 40% 17.3M 3s
13950K .......... .......... .......... .......... .......... 40% 10.2M 3s
14000K .......... .......... .......... .......... .......... 41% 251M 3s
14050K .......... .......... .......... .......... .......... 41% 34.0M 3s
14100K .......... .......... .......... .......... .......... 41% 12.0M 3s
14150K .......... .......... .......... .......... .......... 41% 21.8M 3s
14200K .......... .......... .......... .......... .......... 41% 77.0M 3s
14250K .......... .......... .......... .......... .......... 41% 17.7M 3s
14300K .......... .......... .......... .......... .......... 41% 18.3M 3s
14350K .......... .......... .......... .......... .......... 42% 5.22M 3s
14400K .......... .......... .......... .......... .......... 42% 19.7M 3s
14450K .......... .......... .......... .......... .......... 42% 145M 3s
14500K .......... .......... .......... .......... .......... 42% 117M 3s
14550K .......... .......... .......... .......... .......... 42% 41.2M 3s
14600K .......... .......... .......... .......... .......... 42% 40.1M 3s
14650K .......... .......... .......... .......... .......... 42% 20.9M 3s
14700K .......... .......... .......... .......... .......... 43% 298M 3s
14750K .......... .......... .......... .......... .......... 43% 17.5M 3s
14800K .......... .......... .......... .......... .......... 43% 9.40M 3s
14850K .......... .......... .......... .......... .......... 43% 95.8M 3s
14900K .......... .......... .......... .......... .......... 43% 56.0M 3s
14950K .......... .......... .......... .......... .......... 43% 30.1M 3s
15000K .......... .......... .......... .......... .......... 43% 17.2M 3s
15050K .......... .......... .......... .......... .......... 44% 12.6M 3s
15100K .......... .......... .......... .......... .......... 44% 49.7M 3s
15150K .......... .......... .......... .......... .......... 44% 125M 2s
15200K .......... .......... .......... .......... .......... 44% 22.4M 2s
15250K .......... .......... .......... .......... .......... 44% 7.85M 2s
15300K .......... .......... .......... .......... .......... 44% 16.0M 2s
15350K .......... .......... .......... .......... .......... 44% 16.2M 2s
15400K .......... .......... .......... .......... .......... 45% 9.96M 2s
15450K .......... .......... .......... .......... .......... 45% 78.6M 2s
15500K .......... .......... .......... .......... .......... 45% 11.8M 2s
15550K .......... .......... .......... .......... .......... 45% 9.20M 2s
15600K .......... .......... .......... .......... .......... 45% 28.6M 2s
15650K .......... .......... .......... .......... .......... 45% 10.6M 2s
15700K .......... .......... .......... .......... .......... 45% 12.6M 2s
15750K .......... .......... .......... .......... .......... 46% 11.2M 2s
15800K .......... .......... .......... .......... .......... 46% 12.7M 2s
15850K .......... .......... .......... .......... .......... 46% 133M 2s
15900K .......... .......... .......... .......... .......... 46% 11.5M 2s
15950K .......... .......... .......... .......... .......... 46% 14.2M 2s
16000K .......... .......... .......... .......... .......... 46% 8.47M 2s
16050K .......... .......... .......... .......... .......... 47% 29.1M 2s
16100K .......... .......... .......... .......... .......... 47% 163M 2s
16150K .......... .......... .......... .......... .......... 47% 12.8M 2s
16200K .......... .......... .......... .......... .......... 47% 25.0M 2s
16250K .......... .......... .......... .......... .......... 47% 8.63M 2s
16300K .......... .......... .......... .......... .......... 47% 104M 2s
16350K .......... .......... .......... .......... .......... 47% 26.2M 2s
16400K .......... .......... .......... .......... .......... 48% 8.07M 2s
16450K .......... .......... .......... .......... .......... 48% 72.2M 2s
16500K .......... .......... .......... .......... .......... 48% 17.9M 2s
16550K .......... .......... .......... .......... .......... 48% 13.1M 2s
16600K .......... .......... .......... .......... .......... 48% 24.7M 2s
16650K .......... .......... .......... .......... .......... 48% 15.9M 2s
16700K .......... .......... .......... .......... .......... 48% 12.6M 2s
16750K .......... .......... .......... .......... .......... 49% 53.9M 2s
16800K .......... .......... .......... .......... .......... 49% 64.4M 2s
16850K .......... .......... .......... .......... .......... 49% 7.90M 2s
16900K .......... .......... .......... .......... .......... 49% 103M 2s
16950K .......... .......... .......... .......... .......... 49% 18.8M 2s
17000K .......... .......... .......... .......... .......... 49% 10.6M 2s
17050K .......... .......... .......... .......... .......... 49% 112M 2s
17100K .......... .......... .......... .......... .......... 50% 10.1M 2s
17150K .......... .......... .......... .......... .......... 50% 51.4M 2s
17200K .......... .......... .......... .......... .......... 50% 20.8M 2s
17250K .......... .......... .......... .......... .......... 50% 24.8M 2s
17300K .......... .......... .......... .......... .......... 50% 14.1M 2s
17350K .......... .......... .......... .......... .......... 50% 5.29M 2s
17400K .......... .......... .......... .......... .......... 50% 52.7M 2s
17450K .......... .......... .......... .......... .......... 51% 32.5M 2s
17500K .......... .......... .......... .......... .......... 51% 80.8M 2s
17550K .......... .......... .......... .......... .......... 51% 37.4M 2s
17600K .......... .......... .......... .......... .......... 51% 46.1M 2s
17650K .......... .......... .......... .......... .......... 51% 20.0M 2s
17700K .......... .......... .......... .......... .......... 51% 124M 2s
17750K .......... .......... .......... .......... .......... 51% 57.0M 2s
17800K .......... .......... .......... .......... .......... 52% 21.2M 2s
17850K .......... .......... .......... .......... .......... 52% 10.1M 2s
17900K .......... .......... .......... .......... .......... 52% 33.5M 2s
17950K .......... .......... .......... .......... .......... 52% 140M 2s
18000K .......... .......... .......... .......... .......... 52% 32.6M 2s
18050K .......... .......... .......... .......... .......... 52% 19.4M 2s
18100K .......... .......... .......... .......... .......... 53% 12.3M 2s
18150K .......... .......... .......... .......... .......... 53% 39.9M 2s
18200K .......... .......... .......... .......... .......... 53% 71.6M 2s
18250K .......... .......... .......... .......... .......... 53% 8.75M 2s
18300K .......... .......... .......... .......... .......... 53% 22.0M 2s
18350K .......... .......... .......... .......... .......... 53% 17.4M 2s
18400K .......... .......... .......... .......... .......... 53% 85.1M 2s
18450K .......... .......... .......... .......... .......... 54% 6.07M 2s
18500K .......... .......... .......... .......... .......... 54% 19.8M 2s
18550K .......... .......... .......... .......... .......... 54% 14.4M 2s
18600K .......... .......... .......... .......... .......... 54% 12.5M 2s
18650K .......... .......... .......... .......... .......... 54% 19.9M 2s
18700K .......... .......... .......... .......... .......... 54% 11.8M 2s
18750K .......... .......... .......... .......... .......... 54% 14.6M 2s
18800K .......... .......... .......... .......... .......... 55% 22.5M 2s
18850K .......... .......... .......... .......... .......... 55% 8.13M 2s
18900K .......... .......... .......... .......... .......... 55% 20.1M 2s
18950K .......... .......... .......... .......... .......... 55% 16.3M 2s
19000K .......... .......... .......... .......... .......... 55% 15.7M 2s
19050K .......... .......... .......... .......... .......... 55% 19.5M 2s
19100K .......... .......... .......... .......... .......... 55% 10.8M 2s
19150K .......... .......... .......... .......... .......... 56% 20.0M 2s
19200K .......... .......... .......... .......... .......... 56% 15.2M 2s
19250K .......... .......... .......... .......... .......... 56% 18.7M 2s
19300K .......... .......... .......... .......... .......... 56% 13.4M 2s
19350K .......... .......... .......... .......... .......... 56% 16.6M 2s
19400K .......... .......... .......... .......... .......... 56% 18.9M 2s
19450K .......... .......... .......... .......... .......... 56% 20.3M 2s
19500K .......... .......... .......... .......... .......... 57% 20.0M 2s
19550K .......... .......... .......... .......... .......... 57% 14.4M 2s
19600K .......... .......... .......... .......... .......... 57% 23.1M 2s
19650K .......... .......... .......... .......... .......... 57% 14.4M 2s
19700K .......... .......... .......... .......... .......... 57% 10.9M 2s
19750K .......... .......... .......... .......... .......... 57% 24.3M 2s
19800K .......... .......... .......... .......... .......... 57% 17.0M 2s
19850K .......... .......... .......... .......... .......... 58% 14.7M 2s
19900K .......... .......... .......... .......... .......... 58% 24.8M 2s
19950K .......... .......... .......... .......... .......... 58% 14.5M 2s
20000K .......... .......... .......... .......... .......... 58% 19.4M 2s
20050K .......... .......... .......... .......... .......... 58% 16.7M 2s
20100K .......... .......... .......... .......... .......... 58% 19.5M 2s
20150K .......... .......... .......... .......... .......... 58% 19.8M 2s
20200K .......... .......... .......... .......... .......... 59% 19.5M 2s
20250K .......... .......... .......... .......... .......... 59% 14.4M 2s
20300K .......... .......... .......... .......... .......... 59% 23.4M 2s
20350K .......... .......... .......... .......... .......... 59% 14.4M 2s
20400K .......... .......... .......... .......... .......... 59% 11.2M 2s
20450K .......... .......... .......... .......... .......... 59% 19.7M 2s
20500K .......... .......... .......... .......... .......... 60% 16.7M 2s
20550K .......... .......... .......... .......... .......... 60% 19.2M 2s
20600K .......... .......... .......... .......... .......... 60% 19.7M 2s
20650K .......... .......... .......... .......... .......... 60% 14.0M 2s
20700K .......... .......... .......... .......... .......... 60% 20.8M 2s
20750K .......... .......... .......... .......... .......... 60% 16.4M 1s
20800K .......... .......... .......... .......... .......... 60% 19.3M 1s
20850K .......... .......... .......... .......... .......... 61% 20.0M 1s
20900K .......... .......... .......... .......... .......... 61% 19.4M 1s
20950K .......... .......... .......... .......... .......... 61% 14.5M 1s
21000K .......... .......... .......... .......... .......... 61% 23.9M 1s
21050K .......... .......... .......... .......... .......... 61% 14.4M 1s
21100K .......... .......... .......... .......... .......... 61% 19.5M 1s
21150K .......... .......... .......... .......... .......... 61% 19.9M 1s
21200K .......... .......... .......... .......... .......... 62% 16.6M 1s
21250K .......... .......... .......... .......... .......... 62% 19.2M 1s
21300K .......... .......... .......... .......... .......... 62% 19.8M 1s
21350K .......... .......... .......... .......... .......... 62% 14.5M 1s
21400K .......... .......... .......... .......... .......... 62% 19.2M 1s
21450K .......... .......... .......... .......... .......... 62% 16.7M 1s
21500K .......... .......... .......... .......... .......... 62% 19.6M 1s
21550K .......... .......... .......... .......... .......... 63% 20.0M 1s
21600K .......... .......... .......... .......... .......... 63% 19.5M 1s
21650K .......... .......... .......... .......... .......... 63% 14.4M 1s
21700K .......... .......... .......... .......... .......... 63% 23.5M 1s
21750K .......... .......... .......... .......... .......... 63% 14.2M 1s
21800K .......... .......... .......... .......... .......... 63% 19.8M 1s
21850K .......... .......... .......... .......... .......... 63% 20.2M 1s
21900K .......... .......... .......... .......... .......... 64% 16.4M 1s
21950K .......... .......... .......... .......... .......... 64% 19.0M 1s
22000K .......... .......... .......... .......... .......... 64% 20.2M 1s
22050K .......... .......... .......... .......... .......... 64% 14.1M 1s
22100K .......... .......... .......... .......... .......... 64% 20.0M 1s
22150K .......... .......... .......... .......... .......... 64% 16.6M 1s
22200K .......... .......... .......... .......... .......... 64% 19.7M 1s
22250K .......... .......... .......... .......... .......... 65% 19.7M 1s
22300K .......... .......... .......... .......... .......... 65% 19.8M 1s
22350K .......... .......... .......... .......... .......... 65% 14.2M 1s
22400K .......... .......... .......... .......... .......... 65% 24.0M 1s
22450K .......... .......... .......... .......... .......... 65% 14.4M 1s
22500K .......... .......... .......... .......... .......... 65% 19.4M 1s
22550K .......... .......... .......... .......... .......... 66% 20.1M 1s
22600K .......... .......... .......... .......... .......... 66% 16.4M 1s
22650K .......... .......... .......... .......... .......... 66% 19.3M 1s
22700K .......... .......... .......... .......... .......... 66% 19.7M 1s
22750K .......... .......... .......... .......... .......... 66% 14.3M 1s
22800K .......... .......... .......... .......... .......... 66% 19.5M 1s
22850K .......... .......... .......... .......... .......... 66% 16.9M 1s
22900K .......... .......... .......... .......... .......... 67% 19.4M 1s
22950K .......... .......... .......... .......... .......... 67% 19.7M 1s
23000K .......... .......... .......... .......... .......... 67% 19.7M 1s
23050K .......... .......... .......... .......... .......... 67% 14.0M 1s
23100K .......... .......... .......... .......... .......... 67% 23.7M 1s
23150K .......... .......... .......... .......... .......... 67% 14.2M 1s
23200K .......... .......... .......... .......... .......... 67% 19.8M 1s
23250K .......... .......... .......... .......... .......... 68% 19.7M 1s
23300K .......... .......... .......... .......... .......... 68% 16.4M 1s
23350K .......... .......... .......... .......... .......... 68% 19.5M 1s
23400K .......... .......... .......... .......... .......... 68% 19.2M 1s
23450K .......... .......... .......... .......... .......... 68% 14.5M 1s
23500K .......... .......... .......... .......... .......... 68% 19.4M 1s
23550K .......... .......... .......... .......... .......... 68% 17.3M 1s
23600K .......... .......... .......... .......... .......... 69% 19.4M 1s
23650K .......... .......... .......... .......... .......... 69% 19.2M 1s
23700K .......... .......... .......... .......... .......... 69% 19.8M 1s
23750K .......... .......... .......... .......... .......... 69% 14.1M 1s
23800K .......... .......... .......... .......... .......... 69% 24.2M 1s
23850K .......... .......... .......... .......... .......... 69% 14.1M 1s
23900K .......... .......... .......... .......... .......... 69% 19.9M 1s
23950K .......... .......... .......... .......... .......... 70% 19.7M 1s
24000K .......... .......... .......... .......... .......... 70% 17.0M 1s
24050K .......... .......... .......... .......... .......... 70% 19.4M 1s
24100K .......... .......... .......... .......... .......... 70% 14.5M 1s
24150K .......... .......... .......... .......... .......... 70% 18.9M 1s
24200K .......... .......... .......... .......... .......... 70% 19.8M 1s
24250K .......... .......... .......... .......... .......... 70% 16.7M 1s
24300K .......... .......... .......... .......... .......... 71% 19.1M 1s
24350K .......... .......... .......... .......... .......... 71% 20.2M 1s
24400K .......... .......... .......... .......... .......... 71% 16.4M 1s
24450K .......... .......... .......... .......... .......... 71% 16.6M 1s
24500K .......... .......... .......... .......... .......... 71% 16.9M 1s
24550K .......... .......... .......... .......... .......... 71% 19.7M 1s
24600K .......... .......... .......... .......... .......... 71% 19.0M 1s
24650K .......... .......... .......... .......... .......... 72% 19.8M 1s
24700K .......... .......... .......... .......... .......... 72% 16.5M 1s
24750K .......... .......... .......... .......... .......... 72% 19.3M 1s
24800K .......... .......... .......... .......... .......... 72% 20.3M 1s
24850K .......... .......... .......... .......... .......... 72% 14.1M 1s
24900K .......... .......... .......... .......... .......... 72% 19.9M 1s
24950K .......... .......... .......... .......... .......... 73% 16.9M 1s
25000K .......... .......... .......... .......... .......... 73% 19.3M 1s
25050K .......... .......... .......... .......... .......... 73% 19.1M 1s
25100K .......... .......... .......... .......... .......... 73% 20.0M 1s
25150K .......... .......... .......... .......... .......... 73% 14.4M 1s
25200K .......... .......... .......... .......... .......... 73% 23.3M 1s
25250K .......... .......... .......... .......... .......... 73% 14.5M 1s
25300K .......... .......... .......... .......... .......... 74% 19.4M 1s
25350K .......... .......... .......... .......... .......... 74% 19.8M 1s
25400K .......... .......... .......... .......... .......... 74% 16.9M 1s
25450K .......... .......... .......... .......... .......... 74% 18.7M 1s
25500K .......... .......... .......... .......... .......... 74% 15.0M 1s
25550K .......... .......... .......... .......... .......... 74% 18.9M 1s
25600K .......... .......... .......... .......... .......... 74% 19.7M 1s
25650K .......... .......... .......... .......... .......... 75% 16.9M 1s
25700K .......... .......... .......... .......... .......... 75% 19.1M 1s
25750K .......... .......... .......... .......... .......... 75% 19.4M 1s
25800K .......... .......... .......... .......... .......... 75% 16.9M 1s
25850K .......... .......... .......... .......... .......... 75% 16.5M 1s
25900K .......... .......... .......... .......... .......... 75% 23.8M 1s
25950K .......... .......... .......... .......... .......... 75% 12.6M 1s
26000K .......... .......... .......... .......... .......... 76% 24.2M 1s
26050K .......... .......... .......... .......... .......... 76% 20.0M 1s
26100K .......... .......... .......... .......... .......... 76% 16.8M 1s
26150K .......... .......... .......... .......... .......... 76% 19.0M 1s
26200K .......... .......... .......... .......... .......... 76% 20.0M 1s
26250K .......... .......... .......... .......... .......... 76% 14.0M 1s
26300K .......... .......... .......... .......... .......... 76% 19.7M 1s
26350K .......... .......... .......... .......... .......... 77% 16.9M 1s
26400K .......... .......... .......... .......... .......... 77% 20.0M 1s
26450K .......... .......... .......... .......... .......... 77% 19.3M 1s
26500K .......... .......... .......... .......... .......... 77% 19.5M 1s
26550K .......... .......... .......... .......... .......... 77% 14.5M 1s
26600K .......... .......... .......... .......... .......... 77% 17.1M 1s
26650K .......... .......... .......... .......... .......... 77% 18.7M 1s
26700K .......... .......... .......... .......... .......... 78% 19.4M 1s
26750K .......... .......... .......... .......... .......... 78% 20.2M 1s
26800K .......... .......... .......... .......... .......... 78% 17.5M 1s
26850K .......... .......... .......... .......... .......... 78% 18.6M 1s
26900K .......... .......... .......... .......... .......... 78% 14.2M 1s
26950K .......... .......... .......... .......... .......... 78% 19.6M 1s
27000K .......... .......... .......... .......... .......... 79% 19.4M 1s
27050K .......... .......... .......... .......... .......... 79% 17.6M 1s
27100K .......... .......... .......... .......... .......... 79% 18.1M 1s
27150K .......... .......... .......... .......... .......... 79% 19.7M 1s
27200K .......... .......... .......... .......... .......... 79% 20.2M 1s
27250K .......... .......... .......... .......... .......... 79% 14.3M 1s
27300K .......... .......... .......... .......... .......... 79% 16.8M 1s
27350K .......... .......... .......... .......... .......... 80% 18.8M 1s
27400K .......... .......... .......... .......... .......... 80% 20.0M 1s
27450K .......... .......... .......... .......... .......... 80% 19.7M 1s
27500K .......... .......... .......... .......... .......... 80% 16.4M 1s
27550K .......... .......... .......... .......... .......... 80% 19.9M 1s
27600K .......... .......... .......... .......... .......... 80% 19.2M 1s
27650K .......... .......... .......... .......... .......... 80% 14.4M 1s
27700K .......... .......... .......... .......... .......... 81% 20.0M 1s
27750K .......... .......... .......... .......... .......... 81% 16.8M 1s
27800K .......... .......... .......... .......... .......... 81% 19.4M 1s
27850K .......... .......... .......... .......... .......... 81% 19.0M 1s
27900K .......... .......... .......... .......... .......... 81% 20.1M 1s
27950K .......... .......... .......... .......... .......... 81% 14.2M 1s
28000K .......... .......... .......... .......... .......... 81% 17.5M 1s
28050K .......... .......... .......... .......... .......... 82% 18.4M 1s
28100K .......... .......... .......... .......... .......... 82% 19.6M 1s
28150K .......... .......... .......... .......... .......... 82% 19.9M 1s
28200K .......... .......... .......... .......... .......... 82% 16.6M 1s
28250K .......... .......... .......... .......... .......... 82% 20.2M 1s
28300K .......... .......... .......... .......... .......... 82% 14.0M 1s
28350K .......... .......... .......... .......... .......... 82% 19.6M 1s
28400K .......... .......... .......... .......... .......... 83% 19.4M 1s
28450K .......... .......... .......... .......... .......... 83% 17.7M 1s
28500K .......... .......... .......... .......... .......... 83% 18.4M 1s
28550K .......... .......... .......... .......... .......... 83% 19.7M 1s
28600K .......... .......... .......... .......... .......... 83% 19.8M 1s
28650K .......... .......... .......... .......... .......... 83% 14.3M 1s
28700K .......... .......... .......... .......... .......... 83% 16.4M 1s
28750K .......... .......... .......... .......... .......... 84% 20.0M 1s
28800K .......... .......... .......... .......... .......... 84% 18.8M 1s
28850K .......... .......... .......... .......... .......... 84% 20.1M 1s
28900K .......... .......... .......... .......... .......... 84% 15.9M 1s
28950K .......... .......... .......... .......... .......... 84% 20.2M 0s
29000K .......... .......... .......... .......... .......... 84% 19.9M 0s
29050K .......... .......... .......... .......... .......... 84% 14.4M 0s
29100K .......... .......... .......... .......... .......... 85% 19.7M 0s
29150K .......... .......... .......... .......... .......... 85% 16.6M 0s
29200K .......... .......... .......... .......... .......... 85% 19.5M 0s
29250K .......... .......... .......... .......... .......... 85% 19.8M 0s
29300K .......... .......... .......... .......... .......... 85% 19.3M 0s
29350K .......... .......... .......... .......... .......... 85% 14.6M 0s
29400K .......... .......... .......... .......... .......... 86% 16.8M 0s
29450K .......... .......... .......... .......... .......... 86% 19.1M 0s
29500K .......... .......... .......... .......... .......... 86% 19.6M 0s
29550K .......... .......... .......... .......... .......... 86% 19.9M 0s
29600K .......... .......... .......... .......... .......... 86% 16.5M 0s
29650K .......... .......... .......... .......... .......... 86% 19.5M 0s
29700K .......... .......... .......... .......... .......... 86% 14.6M 0s
29750K .......... .......... .......... .......... .......... 87% 19.2M 0s
29800K .......... .......... .......... .......... .......... 87% 20.0M 0s
29850K .......... .......... .......... .......... .......... 87% 17.6M 0s
29900K .......... .......... .......... .......... .......... 87% 18.0M 0s
29950K .......... .......... .......... .......... .......... 87% 20.0M 0s
30000K .......... .......... .......... .......... .......... 87% 19.8M 0s
30050K .......... .......... .......... .......... .......... 87% 14.2M 0s
30100K .......... .......... .......... .......... .......... 88% 23.8M 0s
30150K .......... .......... .......... .......... .......... 88% 14.2M 0s
30200K .......... .......... .......... .......... .......... 88% 20.0M 0s
30250K .......... .......... .......... .......... .......... 88% 19.5M 0s
30300K .......... .......... .......... .......... .......... 88% 16.7M 0s
30350K .......... .......... .......... .......... .......... 88% 19.7M 0s
30400K .......... .......... .......... .......... .......... 88% 19.5M 0s
30450K .......... .......... .......... .......... .......... 89% 14.3M 0s
30500K .......... .......... .......... .......... .......... 89% 16.6M 0s
30550K .......... .......... .......... .......... .......... 89% 23.0M 0s
30600K .......... .......... .......... .......... .......... 89% 15.7M 0s
30650K .......... .......... .......... .......... .......... 89% 22.3M 0s
30700K .......... .......... .......... .......... .......... 89% 19.5M 0s
30750K .......... .......... .......... .......... .......... 89% 14.3M 0s
30800K .......... .......... .......... .......... .......... 90% 17.3M 0s
30850K .......... .......... .......... .......... .......... 90% 18.0M 0s
30900K .......... .......... .......... .......... .......... 90% 19.6M 0s
30950K .......... .......... .......... .......... .......... 90% 20.5M 0s
31000K .......... .......... .......... .......... .......... 90% 14.2M 0s
31050K .......... .......... .......... .......... .......... 90% 25.0M 0s
31100K .......... .......... .......... .......... .......... 90% 14.5M 0s
31150K .......... .......... .......... .......... .......... 91% 18.6M 0s
31200K .......... .......... .......... .......... .......... 91% 19.9M 0s
31250K .......... .......... .......... .......... .......... 91% 17.2M 0s
31300K .......... .......... .......... .......... .......... 91% 17.5M 0s
31350K .......... .......... .......... .......... .......... 91% 21.1M 0s
31400K .......... .......... .......... .......... .......... 91% 19.8M 0s
31450K .......... .......... .......... .......... .......... 91% 14.5M 0s
31500K .......... .......... .......... .......... .......... 92% 19.3M 0s
31550K .......... .......... .......... .......... .......... 92% 19.4M 0s
31600K .......... .......... .......... .......... .......... 92% 16.6M 0s
31650K .......... .......... .......... .......... .......... 92% 19.9M 0s
31700K .......... .......... .......... .......... .......... 92% 13.9M 0s
31750K .......... .......... .......... .......... .......... 92% 24.1M 0s
31800K .......... .......... .......... .......... .......... 93% 19.7M 0s
31850K .......... .......... .......... .......... .......... 93% 14.3M 0s
31900K .......... .......... .......... .......... .......... 93% 19.4M 0s
31950K .......... .......... .......... .......... .......... 93% 16.7M 0s
32000K .......... .......... .......... .......... .......... 93% 19.8M 0s
32050K .......... .......... .......... .......... .......... 93% 19.3M 0s
32100K .......... .......... .......... .......... .......... 93% 19.5M 0s
32150K .......... .......... .......... .......... .......... 94% 14.6M 0s
32200K .......... .......... .......... .......... .......... 94% 16.7M 0s
32250K .......... .......... .......... .......... .......... 94% 19.4M 0s
32300K .......... .......... .......... .......... .......... 94% 19.3M 0s
32350K .......... .......... .......... .......... .......... 94% 20.0M 0s
32400K .......... .......... .......... .......... .......... 94% 14.3M 0s
32450K .......... .......... .......... .......... .......... 94% 24.8M 0s
32500K .......... .......... .......... .......... .......... 95% 14.3M 0s
32550K .......... .......... .......... .......... .......... 95% 19.0M 0s
32600K .......... .......... .......... .......... .......... 95% 19.8M 0s
32650K .......... .......... .......... .......... .......... 95% 17.1M 0s
32700K .......... .......... .......... .......... .......... 95% 18.8M 0s
32750K .......... .......... .......... .......... .......... 95% 19.8M 0s
32800K .......... .......... .......... .......... .......... 95% 20.0M 0s
32850K .......... .......... .......... .......... .......... 96% 14.4M 0s
32900K .......... .......... .......... .......... .......... 96% 23.5M 0s
32950K .......... .......... .......... .......... .......... 96% 13.6M 0s
33000K .......... .......... .......... .......... .......... 96% 21.0M 0s
33050K .......... .......... .......... .......... .......... 96% 19.9M 0s
33100K .......... .......... .......... .......... .......... 96% 14.4M 0s
33150K .......... .......... .......... .......... .......... 96% 23.8M 0s
33200K .......... .......... .......... .......... .......... 97% 19.7M 0s
33250K .......... .......... .......... .......... .......... 97% 14.2M 0s
33300K .......... .......... .......... .......... .......... 97% 19.7M 0s
33350K .......... .......... .......... .......... .......... 97% 16.8M 0s
33400K .......... .......... .......... .......... .......... 97% 20.5M 0s
33450K .......... .......... .......... .......... .......... 97% 23.5M 0s
33500K .......... .......... .......... .......... .......... 97% 20.5M 0s
33550K .......... .......... .......... .......... .......... 98% 14.5M 0s
33600K .......... .......... .......... .......... .......... 98% 18.7M 0s
33650K .......... .......... .......... .......... .......... 98% 23.4M 0s
33700K .......... .......... .......... .......... .......... 98% 11.6M 0s
33750K .......... .......... .......... .......... .......... 98% 32.0M 0s
33800K .......... .......... .......... .......... .......... 98% 15.4M 0s
33850K .......... .......... .......... .......... .......... 99% 21.8M 0s
33900K .......... .......... .......... .......... .......... 99% 19.4M 0s
33950K .......... .......... .......... .......... .......... 99% 14.3M 0s
34000K .......... .......... .......... .......... .......... 99% 19.6M 0s
34050K .......... .......... .......... .......... .......... 99% 16.4M 0s
34100K .......... .......... .......... .......... .......... 99% 14.9M 0s
34150K .......... .......... .......... .......... .......... 99% 18.9M 0s
34200K .......... .......... .......... ......... 100% 26.8M=3.0s
2021-06-10 06:30:44 (11.0 MB/s) - ‘gromacs-2021.tar.gz’ saved [35061679]
Downloading: https://ftp.gromacs.org/regressiontests/regressiontests-2021.tar.gz
/content/gromacs-2021/build/src/external/build-fftw/fftwBuild-prefix/src/fftwBuild/configure: line 8325: /usr/bin/file: No such file or directory
ar: `u' modifier ignored since `D' is the default (see `U')
ar: `u' modifier ignored since `D' is the default (see `U')
ar: `u' modifier ignored since `D' is the default (see `U')
ar: `u' modifier ignored since `D' is the default (see `U')
ar: `u' modifier ignored since `D' is the default (see `U')
ar: `u' modifier ignored since `D' is the default (see `U')
ar: `u' modifier ignored since `D' is the default (see `U')
ar: `u' modifier ignored since `D' is the default (see `U')
ar: `u' modifier ignored since `D' is the default (see `U')
ar: `u' modifier ignored since `D' is the default (see `U')
ar: `u' modifier ignored since `D' is the default (see `U')
ar: `u' modifier ignored since `D' is the default (see `U')
ar: `u' modifier ignored since `D' is the default (see `U')
ar: `u' modifier ignored since `D' is the default (see `U')
ar: `u' modifier ignored since `D' is the default (see `U')
ar: `u' modifier ignored since `D' is the default (see `U')
ar: `u' modifier ignored since `D' is the default (see `U')
ar: `u' modifier ignored since `D' is the default (see `U')
ar: `u' modifier ignored since `D' is the default (see `U')
ar: `u' modifier ignored since `D' is the default (see `U')
ar: `u' modifier ignored since `D' is the default (see `U')
ar: `u' modifier ignored since `D' is the default (see `U')
In [ ]:
%%bash
source /usr/local/gromacs/bin/GMXRC
#mkdir /content/grojobs
cd new/
gmx
SYNOPSIS
gmx [-[no]h] [-[no]quiet] [-[no]version] [-[no]copyright] [-nice <int>]
[-[no]backup]
OPTIONS
Other options:
-[no]h (no)
Print help and quit
-[no]quiet (no)
Do not print common startup info or quotes
-[no]version (no)
Print extended version information and quit
-[no]copyright (yes)
Print copyright information on startup
-nice <int> (19)
Set the nicelevel (default depends on command)
-[no]backup (yes)
Write backups if output files exist
Additional help is available on the following topics:
commands List of available commands
selections Selection syntax and usage
To access the help, use 'gmx help <topic>'.
For help on a command, use 'gmx help <command>'.
:-) GROMACS - gmx, 2021 (-:
GROMACS is written by:
Andrey Alekseenko Emile Apol Rossen Apostolov
Paul Bauer Herman J.C. Berendsen Par Bjelkmar
Christian Blau Viacheslav Bolnykh Kevin Boyd
Aldert van Buuren Rudi van Drunen Anton Feenstra
Gilles Gouaillardet Alan Gray Gerrit Groenhof
Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
Aleksei Iupinov Christoph Junghans Joe Jordan
Dimitrios Karkoulis Peter Kasson Jiri Kraus
Carsten Kutzner Per Larsson Justin A. Lemkul
Viveca Lindahl Magnus Lundborg Erik Marklund
Pascal Merz Pieter Meulenhoff Teemu Murtola
Szilard Pall Sander Pronk Roland Schulz
Michael Shirts Alexey Shvetsov Alfons Sijbers
Peter Tieleman Jon Vincent Teemu Virolainen
Christian Wennberg Maarten Wolf Artem Zhmurov
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2019, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS: gmx, version 2021
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /content/new
Command line:
gmx
GROMACS reminds you: "Even the *healthy* people move in clouds of cigarette smoke, women straining polyester, men in raggedly cutoffs slathering mayonnaise on foot-long hot dogs. It's as if the hotel were hosting a conference on adult onset diabetes" (Jess Walter)
In [ ]:
!export GMXLIB=/usr/local/share/gromacs/top
## Part 1, from here we will follow the Justin tutorial¶
In [ ]:
!wget http://files.rcsb.org/download/3htb.pdb > prot.pdb
--2021-06-10 07:11:57-- http://files.rcsb.org/download/3htb.pdb Resolving files.rcsb.org (files.rcsb.org)... 132.249.210.222 Connecting to files.rcsb.org (files.rcsb.org)|132.249.210.222|:80... connected. HTTP request sent, awaiting response... 200 OK Length: unspecified [application/octet-stream] Saving to: ‘3htb.pdb’ 3htb.pdb [ <=> ] 162.00K --.-KB/s in 0.1s 2021-06-10 07:11:57 (1.10 MB/s) - ‘3htb.pdb’ saved [165888]
In [ ]:
!grep -v HOH 3htb.pdb > prot_clean.pdb
!grep JZ4 prot_clean.pdb > JZ4.pdb
!grep -v JZ4 prot_clean.pdb > prot_clean2.pdb
!grep -v PO4 prot_clean2.pdb > prot_clean3.pdb
!grep -v BME prot_clean3.pdb > prot_clean4.pdb # here we drop all co-factors to have only protein itself
Beaware that the JZ4.pdb as well as the prot_clean4.pdb do not have any hydrogen atoms yet.
In [ ]:
!wget http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/charmm36-mar2019.ff.tgz
!mv download.php?filename=CHARMM_ff_params_files%2Fcharmm36-mar2019.ff.tgz charmm36-mar2019.ff.tgz
!tar -zxvf charmm36-mar2019.ff.tgz
!rm charmm36-mar2019.ff.tgz
!pwd
--2021-06-10 07:14:56-- http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/charmm36-mar2019.ff.tgz Resolving mackerell.umaryland.edu (mackerell.umaryland.edu)... 134.192.35.52 Connecting to mackerell.umaryland.edu (mackerell.umaryland.edu)|134.192.35.52|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 618813 (604K) [application/x-gzip] Saving to: ‘download.php?filename=CHARMM_ff_params_files%2Fcharmm36-mar2019.ff.tgz’ download.php?filena 100%[===================>] 604.31K 640KB/s in 0.9s 2021-06-10 07:14:57 (640 KB/s) - ‘download.php?filename=CHARMM_ff_params_files%2Fcharmm36-mar2019.ff.tgz’ saved [618813/618813] charmm36-mar2019.ff/ charmm36-mar2019.ff/spc.itp charmm36-mar2019.ff/ffbonded.itp charmm36-mar2019.ff/merged.rtp charmm36-mar2019.ff/nbfix.itp charmm36-mar2019.ff/gb.itp charmm36-mar2019.ff/forcefield.doc charmm36-mar2019.ff/merged.hdb charmm36-mar2019.ff/ions.itp charmm36-mar2019.ff/merged.arn charmm36-mar2019.ff/merged.vsd charmm36-mar2019.ff/spce.itp charmm36-mar2019.ff/old_c36_cmap.itp charmm36-mar2019.ff/ffnonbonded.itp charmm36-mar2019.ff/atomtypes.atp charmm36-mar2019.ff/merged.c.tdb charmm36-mar2019.ff/forcefield.itp charmm36-mar2019.ff/watermodels.dat charmm36-mar2019.ff/tip4p.itp charmm36-mar2019.ff/cmap.itp charmm36-mar2019.ff/merged.n.tdb charmm36-mar2019.ff/tip3p.itp charmm36-mar2019.ff/merged.r2b /content
select option 1(charmm36 force field) and optino 1 (TIP3 water) for next command
In [ ]:
!/usr/local/gromacs/bin/gmx pdb2gmx -f prot_clean4.pdb -o prot_pros.gro
:-) GROMACS - gmx pdb2gmx, 2021 (-:
GROMACS is written by:
Andrey Alekseenko Emile Apol Rossen Apostolov
Paul Bauer Herman J.C. Berendsen Par Bjelkmar
Christian Blau Viacheslav Bolnykh Kevin Boyd
Aldert van Buuren Rudi van Drunen Anton Feenstra
Gilles Gouaillardet Alan Gray Gerrit Groenhof
Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
Aleksei Iupinov Christoph Junghans Joe Jordan
Dimitrios Karkoulis Peter Kasson Jiri Kraus
Carsten Kutzner Per Larsson Justin A. Lemkul
Viveca Lindahl Magnus Lundborg Erik Marklund
Pascal Merz Pieter Meulenhoff Teemu Murtola
Szilard Pall Sander Pronk Roland Schulz
Michael Shirts Alexey Shvetsov Alfons Sijbers
Peter Tieleman Jon Vincent Teemu Virolainen
Christian Wennberg Maarten Wolf Artem Zhmurov
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2019, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS: gmx pdb2gmx, version 2021
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /content
Command line:
gmx pdb2gmx -f prot_clean4.pdb -o prot_pros.gro
Select the Force Field:
From current directory:
1: CHARMM36 all-atom force field (March 2019)
From '/usr/local/gromacs/share/gromacs/top':
2: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)
3: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
4: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996)
5: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000)
6: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006)
7: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010)
8: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
9: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
10: GROMOS96 43a1 force field
11: GROMOS96 43a2 force field (improved alkane dihedrals)
12: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
13: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
14: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
15: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 10.1007/s00249-011-0700-9)
16: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
1
Using the Charmm36-mar2019 force field in directory ./charmm36-mar2019.ff
Opening force field file ./charmm36-mar2019.ff/watermodels.dat
Select the Water Model:
1: TIP3P TIP 3-point, recommended, by default uses CHARMM TIP3 with LJ on H
2: TIP4P TIP 4-point
3: TIP5P TIP 5-point
4: SPC simple point charge
5: SPC/E extended simple point charge
6: None
1
going to rename ./charmm36-mar2019.ff/merged.r2b
Opening force field file ./charmm36-mar2019.ff/merged.r2b
Reading prot_clean4.pdb...
WARNING: all CONECT records are ignored
Read 'LYSOZYME', 1359 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 0 blocks of water and 163 residues with 1359 atoms
chain #res #atoms
1 'A' 163 1359
there were 0 atoms with zero occupancy and 173 atoms with occupancy unequal to one (out of 1359 atoms). Check your pdb file.
there were 0 atoms with zero occupancy and 173 atoms with occupancy unequal to one (out of 1359 atoms). Check your pdb file.
Opening force field file ./charmm36-mar2019.ff/atomtypes.atp
Reading residue database... (Charmm36-mar2019)
Opening force field file ./charmm36-mar2019.ff/merged.rtp
Opening force field file ./charmm36-mar2019.ff/merged.hdb
Opening force field file ./charmm36-mar2019.ff/merged.n.tdb
Opening force field file ./charmm36-mar2019.ff/merged.c.tdb
Processing chain 1 'A' (1359 atoms, 163 residues)
Analysing hydrogen-bonding network for automated assignment of histidine
protonation. 273 donors and 248 acceptors were found.
There are 347 hydrogen bonds
Will use HISD for residue 31
Identified residue MET1 as a starting terminus.
Identified residue ASN163 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
MET1 MET6 HIS31 CYS54 CYS97 MET106
SD7 SD51 NE2271 SG441 SG803 SD878
MET6 SD51 0.631
HIS31 NE2271 2.196 1.931
CYS54 SG441 2.781 2.718 1.052
CYS97 SG803 0.820 0.539 2.117 2.897
MET106 SD878 1.900 1.314 1.848 2.841 1.635
MET120 SD977 2.525 2.014 3.286 4.293 2.112 1.520
Start terminus MET-1: NH3+
End terminus ASN-163: COO-
Opening force field file ./charmm36-mar2019.ff/merged.arn
Checking for duplicate atoms....
Now there are 1300 atoms. Deleted 59 duplicates.
Generating any missing hydrogen atoms and/or adding termini.
Now there are 163 residues with 2614 atoms
Making bonds...
Number of bonds was 2634, now 2634
Generating angles, dihedrals and pairs...
Before cleaning: 6889 pairs
Before cleaning: 6924 dihedrals
Keeping all generated dihedrals
Making cmap torsions...
There are 161 cmap torsion pairs
There are 6924 dihedrals, 458 impropers, 4751 angles
6847 pairs, 2634 bonds and 0 virtual sites
Total mass 18512.245 a.m.u.
Total charge 6.000 e
Writing topology
Writing coordinate file...
--------- PLEASE NOTE ------------
You have successfully generated a topology from: prot_clean4.pdb.
The Charmm36-mar2019 force field and the tip3p water model are used.
--------- ETON ESAELP ------------
GROMACS reminds you: "Push It Real Good" (Salt 'n' Pepa)
In [ ]:
!tail topol.top
; Include topology for ions #include "./charmm36-mar2019.ff/ions.itp" [ system ] ; Name LYSOZYME [ molecules ] ; Compound #mols Protein_chain_A 1
Download and compile Obabel¶
In [ ]:
!wget https://github.com/openbabel/openbabel/archive/refs/tags/openbabel-3-1-1.tar.gz
!tar -xzvf openbabel-3-1-1.tar.gz
%cd openbabel-openbabel-3-1-1/
!ls
!mkdir build
%cd build
!cmake ../
!make
!make install
%cd /content/
/content
In [ ]:
!obabel -ipdb JZ4.pdb -omol2 -O jz4.mol2 -h # convert the format and add hydrogen atoms
1 molecule converted
In [ ]:
!sed -i 's/JZ4.pdb/JZ4/' jz4.mol2
In [ ]:
!cat jz4.mol2
@<TRIPOS>MOLECULE
JZ4
22 22 0 0 0
SMALL
GASTEIGER
@<TRIPOS>ATOM
1 C4 24.2940 -24.1240 -0.0710 C.3 167 JZ4167 -0.0650
2 C7 21.5530 -27.2140 -4.1120 C.ar 167 JZ4167 -0.0613
3 C8 22.0680 -26.7470 -5.3310 C.ar 167 JZ4167 -0.0583
4 C9 22.6710 -25.5120 -5.4480 C.ar 167 JZ4167 -0.0199
5 C10 22.7690 -24.7300 -4.2950 C.ar 167 JZ4167 0.1200
6 C11 21.6930 -26.4590 -2.9540 C.ar 167 JZ4167 -0.0551
7 C12 22.2940 -25.1870 -3.0750 C.ar 167 JZ4167 -0.0060
8 C13 22.4630 -24.4140 -1.8080 C.3 167 JZ4167 -0.0245
9 C14 23.9250 -24.7040 -1.3940 C.3 167 JZ4167 -0.0518
10 OAB 23.4120 -23.5360 -4.3420 O.3 167 JZ4167 -0.5065
11 H 25.3133 -24.3619 0.1509 H 167 JZ4167 0.0230
12 H 23.6591 -24.5327 0.6872 H 167 JZ4167 0.0230
13 H 24.1744 -23.0611 -0.1016 H 167 JZ4167 0.0230
14 H 21.0673 -28.1238 -4.0754 H 167 JZ4167 0.0618
15 H 21.9931 -27.3472 -6.1672 H 167 JZ4167 0.0619
16 H 23.0361 -25.1783 -6.3537 H 167 JZ4167 0.0654
17 H 21.3701 -26.8143 -2.0405 H 167 JZ4167 0.0621
18 H 21.7794 -24.7551 -1.0588 H 167 JZ4167 0.0314
19 H 22.2659 -23.3694 -1.9301 H 167 JZ4167 0.0314
20 H 24.5755 -24.2929 -2.1375 H 167 JZ4167 0.0266
21 H 24.0241 -25.7662 -1.3110 H 167 JZ4167 0.0266
22 H 23.7394 -23.2120 -5.1580 H 167 JZ4167 0.2921
@<TRIPOS>BOND
1 4 3 ar
2 4 5 ar
3 3 2 ar
4 10 5 1
5 5 7 ar
6 2 6 ar
7 7 6 ar
8 7 8 1
9 8 9 1
10 9 1 1
11 1 11 1
12 1 12 1
13 1 13 1
14 2 14 1
15 3 15 1
16 4 16 1
17 6 17 1
18 8 18 1
19 8 19 1
20 9 20 1
21 9 21 1
22 10 22 1
In [ ]:
!wget http://www.mdtutorials.com/gmx/complex/Files/sort_mol2_bonds.pl
!perl sort_mol2_bonds.pl jz4.mol2 jz4_fix.mol2
--2021-06-10 07:25:53-- http://www.mdtutorials.com/gmx/complex/Files/sort_mol2_bonds.pl Resolving www.mdtutorials.com (www.mdtutorials.com)... 13.59.3.21 Connecting to www.mdtutorials.com (www.mdtutorials.com)|13.59.3.21|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 3490 (3.4K) [text/x-perl] Saving to: ‘sort_mol2_bonds.pl’ sort_mol2_bonds.pl 100%[===================>] 3.41K --.-KB/s in 0s 2021-06-10 07:25:53 (458 MB/s) - ‘sort_mol2_bonds.pl’ saved [3490/3490] Found 22 atoms in the molecule, with 22 bonds.
In [ ]:
!cat jz4_fix.mol2 # pay attention to the bond order section
@<TRIPOS>MOLECULE
JZ4
22 22 0 0 0
SMALL
GASTEIGER
@<TRIPOS>ATOM
1 C4 24.2940 -24.1240 -0.0710 C.3 167 JZ4167 -0.0650
2 C7 21.5530 -27.2140 -4.1120 C.ar 167 JZ4167 -0.0613
3 C8 22.0680 -26.7470 -5.3310 C.ar 167 JZ4167 -0.0583
4 C9 22.6710 -25.5120 -5.4480 C.ar 167 JZ4167 -0.0199
5 C10 22.7690 -24.7300 -4.2950 C.ar 167 JZ4167 0.1200
6 C11 21.6930 -26.4590 -2.9540 C.ar 167 JZ4167 -0.0551
7 C12 22.2940 -25.1870 -3.0750 C.ar 167 JZ4167 -0.0060
8 C13 22.4630 -24.4140 -1.8080 C.3 167 JZ4167 -0.0245
9 C14 23.9250 -24.7040 -1.3940 C.3 167 JZ4167 -0.0518
10 OAB 23.4120 -23.5360 -4.3420 O.3 167 JZ4167 -0.5065
11 H 25.3133 -24.3619 0.1509 H 167 JZ4167 0.0230
12 H 23.6591 -24.5327 0.6872 H 167 JZ4167 0.0230
13 H 24.1744 -23.0611 -0.1016 H 167 JZ4167 0.0230
14 H 21.0673 -28.1238 -4.0754 H 167 JZ4167 0.0618
15 H 21.9931 -27.3472 -6.1672 H 167 JZ4167 0.0619
16 H 23.0361 -25.1783 -6.3537 H 167 JZ4167 0.0654
17 H 21.3701 -26.8143 -2.0405 H 167 JZ4167 0.0621
18 H 21.7794 -24.7551 -1.0588 H 167 JZ4167 0.0314
19 H 22.2659 -23.3694 -1.9301 H 167 JZ4167 0.0314
20 H 24.5755 -24.2929 -2.1375 H 167 JZ4167 0.0266
21 H 24.0241 -25.7662 -1.3110 H 167 JZ4167 0.0266
22 H 23.7394 -23.2120 -5.1580 H 167 JZ4167 0.2921
@<TRIPOS>BOND
1 1 9 1
2 1 11 1
3 1 12 1
4 1 13 1
5 2 3 ar
6 2 6 ar
7 2 14 1
8 3 4 ar
9 3 15 1
10 4 5 ar
11 4 16 1
12 5 10 1
13 5 7 ar
14 6 7 ar
15 6 17 1
16 7 8 1
17 8 9 1
18 8 18 1
19 8 19 1
20 9 20 1
21 9 21 1
22 10 22 1
In [ ]:
!touch jz4.txt # the only reason I use text format is it can be directly open upon double clik on the right.
Download the jz4_fix.mol2 and updoad to CGenff server¶
Then paste the result to the mannually touched jz4.txt, then rename to jz4.str https://cgenff.umaryland.edu/userAccount/userLogin.php¶
In [ ]:
!head jz4.txt
* Toppar stream file generated by * CHARMM General Force Field (CGenFF) program version 2.4.0 * For use with CGenFF version 4.4 * read rtf card append * Topologies generated by * CHARMM General Force Field (CGenFF) program version 2.4.0 * 36 1
In [ ]:
!mv jz4.txt jz4.str
!wget http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/cgenff_charmm2gmx_py3_nx2.py
!mv download.php\?filename\=CHARMM_ff_params_files%2Fcgenff_charmm2gmx_py3_nx2.py cgenff_charmm2gmx_py3_nx2.py
--2021-06-10 07:40:53-- http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/cgenff_charmm2gmx_py3_nx2.py Resolving mackerell.umaryland.edu (mackerell.umaryland.edu)... 134.192.35.52 Connecting to mackerell.umaryland.edu (mackerell.umaryland.edu)|134.192.35.52|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 37837 (37K) [text/x-python] Saving to: ‘download.php?filename=CHARMM_ff_params_files%2Fcgenff_charmm2gmx_py3_nx2.py’ download.php?filena 100%[===================>] 36.95K --.-KB/s in 0.08s 2021-06-10 07:40:53 (481 KB/s) - ‘download.php?filename=CHARMM_ff_params_files%2Fcgenff_charmm2gmx_py3_nx2.py’ saved [37837/37837]
You also need to input yes for the next command¶
In [ ]:
!pip uninstall networkx
!pip install networkx==2.3
Uninstalling networkx-2.5.1:
Would remove:
/usr/local/lib/python3.7/dist-packages/networkx-2.5.1.dist-info/*
/usr/local/lib/python3.7/dist-packages/networkx/*
/usr/local/share/doc/networkx-2.5.1/LICENSE.txt
/usr/local/share/doc/networkx-2.5.1/examples/3d_drawing/README.txt
/usr/local/share/doc/networkx-2.5.1/examples/3d_drawing/mayavi2_spring.py
/usr/local/share/doc/networkx-2.5.1/examples/README.txt
/usr/local/share/doc/networkx-2.5.1/examples/advanced/README.txt
/usr/local/share/doc/networkx-2.5.1/examples/advanced/plot_eigenvalues.py
/usr/local/share/doc/networkx-2.5.1/examples/advanced/plot_heavy_metal_umlaut.py
/usr/local/share/doc/networkx-2.5.1/examples/advanced/plot_iterated_dynamical_systems.py
/usr/local/share/doc/networkx-2.5.1/examples/advanced/plot_parallel_betweenness.py
/usr/local/share/doc/networkx-2.5.1/examples/algorithms/README.txt
/usr/local/share/doc/networkx-2.5.1/examples/algorithms/hartford_drug.edgelist
/usr/local/share/doc/networkx-2.5.1/examples/algorithms/plot_beam_search.py
/usr/local/share/doc/networkx-2.5.1/examples/algorithms/plot_blockmodel.py
/usr/local/share/doc/networkx-2.5.1/examples/algorithms/plot_davis_club.py
/usr/local/share/doc/networkx-2.5.1/examples/algorithms/plot_decomposition.py
/usr/local/share/doc/networkx-2.5.1/examples/algorithms/plot_krackhardt_centrality.py
/usr/local/share/doc/networkx-2.5.1/examples/algorithms/plot_rcm.py
/usr/local/share/doc/networkx-2.5.1/examples/basic/README.txt
/usr/local/share/doc/networkx-2.5.1/examples/basic/plot_properties.py
/usr/local/share/doc/networkx-2.5.1/examples/basic/plot_read_write.py
/usr/local/share/doc/networkx-2.5.1/examples/drawing/README.txt
/usr/local/share/doc/networkx-2.5.1/examples/drawing/chess_masters_WCC.pgn.bz2
/usr/local/share/doc/networkx-2.5.1/examples/drawing/knuth_miles.txt.gz
/usr/local/share/doc/networkx-2.5.1/examples/drawing/lanl_routes.edgelist
/usr/local/share/doc/networkx-2.5.1/examples/drawing/plot_atlas.py
/usr/local/share/doc/networkx-2.5.1/examples/drawing/plot_chess_masters.py
/usr/local/share/doc/networkx-2.5.1/examples/drawing/plot_circular_tree.py
/usr/local/share/doc/networkx-2.5.1/examples/drawing/plot_degree_histogram.py
/usr/local/share/doc/networkx-2.5.1/examples/drawing/plot_degree_rank.py
/usr/local/share/doc/networkx-2.5.1/examples/drawing/plot_directed.py
/usr/local/share/doc/networkx-2.5.1/examples/drawing/plot_edge_colormap.py
/usr/local/share/doc/networkx-2.5.1/examples/drawing/plot_ego_graph.py
/usr/local/share/doc/networkx-2.5.1/examples/drawing/plot_four_grids.py
/usr/local/share/doc/networkx-2.5.1/examples/drawing/plot_giant_component.py
/usr/local/share/doc/networkx-2.5.1/examples/drawing/plot_house_with_colors.py
/usr/local/share/doc/networkx-2.5.1/examples/drawing/plot_knuth_miles.py
/usr/local/share/doc/networkx-2.5.1/examples/drawing/plot_labels_and_colors.py
/usr/local/share/doc/networkx-2.5.1/examples/drawing/plot_lanl_routes.py
/usr/local/share/doc/networkx-2.5.1/examples/drawing/plot_multipartite_graph.py
/usr/local/share/doc/networkx-2.5.1/examples/drawing/plot_node_colormap.py
/usr/local/share/doc/networkx-2.5.1/examples/drawing/plot_random_geometric_graph.py
/usr/local/share/doc/networkx-2.5.1/examples/drawing/plot_sampson.py
/usr/local/share/doc/networkx-2.5.1/examples/drawing/plot_simple_path.py
/usr/local/share/doc/networkx-2.5.1/examples/drawing/plot_spectral_grid.py
/usr/local/share/doc/networkx-2.5.1/examples/drawing/plot_unix_email.py
/usr/local/share/doc/networkx-2.5.1/examples/drawing/plot_weighted_graph.py
/usr/local/share/doc/networkx-2.5.1/examples/drawing/unix_email.mbox
/usr/local/share/doc/networkx-2.5.1/examples/graph/README.txt
/usr/local/share/doc/networkx-2.5.1/examples/graph/dot_atlas.py
/usr/local/share/doc/networkx-2.5.1/examples/graph/plot_degree_sequence.py
/usr/local/share/doc/networkx-2.5.1/examples/graph/plot_erdos_renyi.py
/usr/local/share/doc/networkx-2.5.1/examples/graph/plot_expected_degree_sequence.py
/usr/local/share/doc/networkx-2.5.1/examples/graph/plot_football.py
/usr/local/share/doc/networkx-2.5.1/examples/graph/plot_karate_club.py
/usr/local/share/doc/networkx-2.5.1/examples/graph/plot_napoleon_russian_campaign.py
/usr/local/share/doc/networkx-2.5.1/examples/graph/plot_roget.py
/usr/local/share/doc/networkx-2.5.1/examples/graph/plot_words.py
/usr/local/share/doc/networkx-2.5.1/examples/graph/roget_dat.txt.gz
/usr/local/share/doc/networkx-2.5.1/examples/graph/words_dat.txt.gz
/usr/local/share/doc/networkx-2.5.1/examples/javascript/README.txt
/usr/local/share/doc/networkx-2.5.1/examples/javascript/force.py
/usr/local/share/doc/networkx-2.5.1/examples/javascript/force/README.txt
/usr/local/share/doc/networkx-2.5.1/examples/javascript/force/force.css
/usr/local/share/doc/networkx-2.5.1/examples/javascript/force/force.html
/usr/local/share/doc/networkx-2.5.1/examples/javascript/force/force.js
/usr/local/share/doc/networkx-2.5.1/examples/jit/README.txt
/usr/local/share/doc/networkx-2.5.1/examples/jit/plot_rgraph.py
/usr/local/share/doc/networkx-2.5.1/examples/pygraphviz/README.txt
/usr/local/share/doc/networkx-2.5.1/examples/pygraphviz/plot_pygraphviz_attributes.py
/usr/local/share/doc/networkx-2.5.1/examples/pygraphviz/plot_pygraphviz_draw.py
/usr/local/share/doc/networkx-2.5.1/examples/pygraphviz/plot_pygraphviz_simple.py
/usr/local/share/doc/networkx-2.5.1/examples/pygraphviz/plot_write_dotfile.py
/usr/local/share/doc/networkx-2.5.1/examples/subclass/README.txt
/usr/local/share/doc/networkx-2.5.1/examples/subclass/plot_antigraph.py
/usr/local/share/doc/networkx-2.5.1/examples/subclass/plot_printgraph.py
/usr/local/share/doc/networkx-2.5.1/requirements.txt
Proceed (y/n)? y
Successfully uninstalled networkx-2.5.1
Collecting networkx==2.3
Downloading https://files.pythonhosted.org/packages/85/08/f20aef11d4c343b557e5de6b9548761811eb16e438cee3d32b1c66c8566b/networkx-2.3.zip (1.7MB)
|████████████████████████████████| 1.8MB 8.4MB/s
Requirement already satisfied: decorator>=4.3.0 in /usr/local/lib/python3.7/dist-packages (from networkx==2.3) (4.4.2)
Building wheels for collected packages: networkx
Building wheel for networkx (setup.py) ... done
Created wheel for networkx: filename=networkx-2.3-py2.py3-none-any.whl size=1556427 sha256=43f25fda0ff1e9ad030d29861ea5ddacec083281c850d4265ea46bdc2cec1c05
Stored in directory: /root/.cache/pip/wheels/de/63/64/3699be2a9d0ccdb37c7f16329acf3863fd76eda58c39c737af
Successfully built networkx
ERROR: albumentations 0.1.12 has requirement imgaug<0.2.7,>=0.2.5, but you'll have imgaug 0.2.9 which is incompatible.
Installing collected packages: networkx
Successfully installed networkx-2.3
There might be an error, but that shouldn't influence this simulation job, so just ignore it.
In [ ]:
%%bash
python cgenff_charmm2gmx_py3_nx2.py JZ4 jz4_fix.mol2 jz4.str charmm36-mar2019.ff
NOTE 1: Code tested with Python 3.5.2 and 3.7.3. Your version: 3.7.10 (default, May 3 2021, 02:48:31) [GCC 7.5.0] NOTE 2: Code tested with NetworkX 2.3. Your version: 2.3 NOTE 3: Please be sure to use the same version of CGenFF in your simulations that was used during parameter generation: --Version of CGenFF detected in jz4.str : 4.4 --Version of CGenFF detected in charmm36-mar2019.ff/forcefield.doc : 4.1 WARNING: CGenFF versions are not equivalent! NOTE 4: To avoid duplicated parameters, do NOT select the 'Include parameters that are already in CGenFF' option when uploading a molecule into CGenFF. ============ DONE ============ Conversion complete. The molecule topology has been written to jz4.itp Additional parameters needed by the molecule are written to jz4.prm, which needs to be included in the system .top PLEASE NOTE: If your topology has lone pairs, you must use GROMACS version 2020 or newer to use 2fd construction Older GROMACS versions WILL NOT WORK as they do not support 2fd virtual site construction ============ DONE ============
After this, the output jz4_ini.pdb contains all the 22 atoms of the ligand JZ4
In [ ]:
!/usr/local/gromacs/bin/gmx editconf -f jz4_ini.pdb -o jz4.gro
:-) GROMACS - gmx editconf, 2021 (-:
GROMACS is written by:
Andrey Alekseenko Emile Apol Rossen Apostolov
Paul Bauer Herman J.C. Berendsen Par Bjelkmar
Christian Blau Viacheslav Bolnykh Kevin Boyd
Aldert van Buuren Rudi van Drunen Anton Feenstra
Gilles Gouaillardet Alan Gray Gerrit Groenhof
Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
Aleksei Iupinov Christoph Junghans Joe Jordan
Dimitrios Karkoulis Peter Kasson Jiri Kraus
Carsten Kutzner Per Larsson Justin A. Lemkul
Viveca Lindahl Magnus Lundborg Erik Marklund
Pascal Merz Pieter Meulenhoff Teemu Murtola
Szilard Pall Sander Pronk Roland Schulz
Michael Shirts Alexey Shvetsov Alfons Sijbers
Peter Tieleman Jon Vincent Teemu Virolainen
Christian Wennberg Maarten Wolf Artem Zhmurov
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2019, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS: gmx editconf, version 2021
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /content
Command line:
gmx editconf -f jz4_ini.pdb -o jz4.gro
Note that major changes are planned in future for editconf, to improve usability and utility.
Read 22 atoms
No velocities found
GROMACS reminds you: "It was something to at least have a choice of nightmares" (Joseph Conrad)
Let's have a look at jz4.gro
In [ ]:
!cat jz4.gro
Gnomes, ROck Monsters And Chili Sauce
22
1JZ4 C4 1 2.429 -2.412 -0.007
1JZ4 C7 2 2.155 -2.721 -0.411
1JZ4 C8 3 2.207 -2.675 -0.533
1JZ4 C9 4 2.267 -2.551 -0.545
1JZ4 C10 5 2.277 -2.473 -0.430
1JZ4 C11 6 2.169 -2.646 -0.295
1JZ4 C12 7 2.229 -2.519 -0.308
1JZ4 C13 8 2.246 -2.441 -0.181
1JZ4 C14 9 2.392 -2.470 -0.139
1JZ4 OAB 10 2.341 -2.354 -0.434
1JZ4 H1 11 2.531 -2.436 0.015
1JZ4 H2 12 2.366 -2.453 0.069
1JZ4 H3 13 2.417 -2.306 -0.010
1JZ4 H4 14 2.107 -2.812 -0.407
1JZ4 H5 15 2.199 -2.735 -0.617
1JZ4 H6 16 2.304 -2.518 -0.635
1JZ4 H7 17 2.137 -2.681 -0.204
1JZ4 H8 18 2.178 -2.476 -0.106
1JZ4 H9 19 2.227 -2.337 -0.193
1JZ4 H10 20 2.458 -2.429 -0.214
1JZ4 H11 21 2.402 -2.577 -0.131
1JZ4 H12 22 2.374 -2.321 -0.516
0.00000 0.00000 0.00000
Please be advised you double check the command line has acturally worked, some time you hit the triangle but the result maybe in a russ to write and save to the file as we here all deal with online things, if at that moment your connection is slow, then there is a chance you may fail the command.
Combine protein and ligand¶
In [ ]:
!cat prot_pros.gro > complex.gro
Always have a look at the file you just produced,there should be 2614 atoms inside
In [ ]:
!cat complex.gro
5.99500 5.19182 9.66100 0.00000 0.00000 -2.99750 0.00000 0.00000 0.00000
In [ ]:
!tail -1 complex.gro > last_line.txt
In [ ]:
!cat last_line.txt
5.99500 5.19182 9.66100 0.00000 0.00000 -2.99750 0.00000 0.00000 0.00000
In [ ]:
!head -n -1 complex.gro > temp.txt
In [ ]:
!cat temp.txt
163ASN OT2 2614 0.683 -0.703 -0.011
There still 2614 atoms inside temp.txt but the last line of box vector is moved out temperarily.
Let's combine jz4.gro and complex.gro now
In [ ]:
!cat jz4.gro
Gnomes, ROck Monsters And Chili Sauce
22
1JZ4 C4 1 2.429 -2.412 -0.007
1JZ4 C7 2 2.155 -2.721 -0.411
1JZ4 C8 3 2.207 -2.675 -0.533
1JZ4 C9 4 2.267 -2.551 -0.545
1JZ4 C10 5 2.277 -2.473 -0.430
1JZ4 C11 6 2.169 -2.646 -0.295
1JZ4 C12 7 2.229 -2.519 -0.308
1JZ4 C13 8 2.246 -2.441 -0.181
1JZ4 C14 9 2.392 -2.470 -0.139
1JZ4 OAB 10 2.341 -2.354 -0.434
1JZ4 H1 11 2.531 -2.436 0.015
1JZ4 H2 12 2.366 -2.453 0.069
1JZ4 H3 13 2.417 -2.306 -0.010
1JZ4 H4 14 2.107 -2.812 -0.407
1JZ4 H5 15 2.199 -2.735 -0.617
1JZ4 H6 16 2.304 -2.518 -0.635
1JZ4 H7 17 2.137 -2.681 -0.204
1JZ4 H8 18 2.178 -2.476 -0.106
1JZ4 H9 19 2.227 -2.337 -0.193
1JZ4 H10 20 2.458 -2.429 -0.214
1JZ4 H11 21 2.402 -2.577 -0.131
1JZ4 H12 22 2.374 -2.321 -0.516
0.00000 0.00000 0.00000
In [ ]:
!grep JZ4 jz4.gro >> temp.txt
Let's have a look at if the ligand atoms have been added after the protein atoms
In [ ]:
!cat temp.txt
1JZ4 H12 22 2.374 -2.321 -0.516
Next let's add the box vector back to the last line.
In [ ]:
!cat last_line.txt >> temp.txt
In [ ]:
!head -10 temp.txt
LYSOZYME
2614
1MET N 1 0.556 -1.596 -0.893
1MET H1 2 0.522 -1.511 -0.855
1MET H2 3 0.520 -1.608 -0.986
1MET H3 4 0.527 -1.673 -0.836
1MET CA 5 0.704 -1.593 -0.898
1MET HA 6 0.731 -1.519 -0.960
1MET CB 7 0.763 -1.561 -0.758
1MET HB1 8 0.710 -1.486 -0.719
In [ ]:
!tail -30 temp.txt
163ASN CG 2607 0.826 -0.677 -0.388
163ASN OD1 2608 0.718 -0.644 -0.435
163ASN ND2 2609 0.943 -0.641 -0.442
163ASN HD21 2610 1.029 -0.671 -0.401
163ASN HD22 2611 0.944 -0.584 -0.525
163ASN C 2612 0.621 -0.740 -0.126
163ASN OT1 2613 0.624 -0.616 -0.140
163ASN OT2 2614 0.683 -0.703 -0.011
1JZ4 C4 1 2.429 -2.412 -0.007
1JZ4 C7 2 2.155 -2.721 -0.411
1JZ4 C8 3 2.207 -2.675 -0.533
1JZ4 C9 4 2.267 -2.551 -0.545
1JZ4 C10 5 2.277 -2.473 -0.430
1JZ4 C11 6 2.169 -2.646 -0.295
1JZ4 C12 7 2.229 -2.519 -0.308
1JZ4 C13 8 2.246 -2.441 -0.181
1JZ4 C14 9 2.392 -2.470 -0.139
1JZ4 OAB 10 2.341 -2.354 -0.434
1JZ4 H1 11 2.531 -2.436 0.015
1JZ4 H2 12 2.366 -2.453 0.069
1JZ4 H3 13 2.417 -2.306 -0.010
1JZ4 H4 14 2.107 -2.812 -0.407
1JZ4 H5 15 2.199 -2.735 -0.617
1JZ4 H6 16 2.304 -2.518 -0.635
1JZ4 H7 17 2.137 -2.681 -0.204
1JZ4 H8 18 2.178 -2.476 -0.106
1JZ4 H9 19 2.227 -2.337 -0.193
1JZ4 H10 20 2.458 -2.429 -0.214
1JZ4 H11 21 2.402 -2.577 -0.131
1JZ4 H12 22 2.374 -2.321 -0.516
Finally we need to increase the atom number claim
In [ ]:
!sed -i '2s/2614/2636/' temp.txt
In [ ]:
!head -10 temp.txt
LYSOZYME
2636
1MET N 1 0.556 -1.596 -0.893
1MET H1 2 0.522 -1.511 -0.855
1MET H2 3 0.520 -1.608 -0.986
1MET H3 4 0.527 -1.673 -0.836
1MET CA 5 0.704 -1.593 -0.898
1MET HA 6 0.731 -1.519 -0.960
1MET CB 7 0.763 -1.561 -0.758
1MET HB1 8 0.710 -1.486 -0.719
In [ ]:
!cat temp.txt > complex.gro # I use cat instead of mv, just to keep the temp.txt copy in case later we need it.
In [ ]:
!head complex.gro
LYSOZYME
2636
1MET N 1 0.556 -1.596 -0.893
1MET H1 2 0.522 -1.511 -0.855
1MET H2 3 0.520 -1.608 -0.986
1MET H3 4 0.527 -1.673 -0.836
1MET CA 5 0.704 -1.593 -0.898
1MET HA 6 0.731 -1.519 -0.960
1MET CB 7 0.763 -1.561 -0.758
1MET HB1 8 0.710 -1.486 -0.719
Fix the topol.top¶
In [ ]:
!cat topol.top > topol.txt
In [ ]:
!tail -25 topol.txt
; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif ; Include water topology #include "./charmm36-mar2019.ff/tip3p.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include topology for ions #include "./charmm36-mar2019.ff/ions.itp" [ system ] ; Name LYSOZYME [ molecules ] ; Compound #mols Protein_chain_A 1
In [ ]:
!sed -i "/; Include water topology/ { N; s/; Include water topology\n/; Include ligand topology #include "jz4.itp"\n&/ }" topol.txt
you shoud see there is one more line before "Include water topology" now you need to put "#inclue "jz4.inp" to the next line. Pay attention to the " ", since they are likely to be missed out.
In [ ]:
!tail -25 topol.txt
#include "posre.itp" #endif ; Include ligand topology #include "jz4.itp" ; Include water topology #include "./charmm36-mar2019.ff/tip3p.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include topology for ions #include "./charmm36-mar2019.ff/ions.itp" [ system ] ; Name LYSOZYME [ molecules ] ; Compound #mols Protein_chain_A 1
Please make sure you have put the following before Include water topology.
; Include ligand topology
#include "jz4.itp"In [ ]:
!tail -25 topol.txt
#include "posre.itp" #endif ; Include ligand topology #include "jz4.itp" ; Include water topology #include "./charmm36-mar2019.ff/tip3p.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include topology for ions #include "./charmm36-mar2019.ff/ions.itp" [ system ] ; Name LYSOZYME [ molecules ] ; Compound #mols Protein_chain_A 1
In [ ]:
!echo "JZ4 1" >> topol.txt
In [ ]:
!tail -25 topol.txt
#endif ; Include ligand topology #include "jz4.itp" ; Include water topology #include "./charmm36-mar2019.ff/tip3p.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include topology for ions #include "./charmm36-mar2019.ff/ions.itp" [ system ] ; Name LYSOZYME [ molecules ] ; Compound #mols Protein_chain_A 1 JZ4 1
Now you should notice there is one more line at the end
Protein_chain_A 1manually insert the another block,
; Include ligand parameters
#include "jz4.prm"before [moleculetype]
In [ ]:
!head -30 topol.txt
; ; File 'topol.top' was generated ; By user: unknown (0) ; On host: ce0e39246148 ; At date: Thu Jun 10 07:15:37 2021 ; ; This is a standalone topology file ; ; Created by: ; :-) GROMACS - gmx pdb2gmx, 2021 (-: ; ; Executable: /usr/local/gromacs/bin/gmx ; Data prefix: /usr/local/gromacs ; Working dir: /content ; Command line: ; gmx pdb2gmx -f prot_clean4.pdb -o prot_pros.gro ; Force field was read from current directory or a relative path - path added. ; ; Include forcefield parameters #include "./charmm36-mar2019.ff/forcefield.itp" ; Include ligand parameters #include "jz4.prm" [ moleculetype ] ; Name nrexcl Protein_chain_A 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB
In [ ]:
!cat topol.txt > topol.top # again, here I used cat instead of mv to keep topol.txt as an extra copy in case there might be an error later
Let's double check the topol.top
In [ ]:
!cat topol.top
JZ4 1
Now time for Gromacs!¶
In [ ]:
!/usr/local/gromacs/bin/gmx editconf -f complex.gro -o newbox.gro -bt dodecahedron -d 1.0
:-) GROMACS - gmx editconf, 2021 (-:
GROMACS is written by:
Andrey Alekseenko Emile Apol Rossen Apostolov
Paul Bauer Herman J.C. Berendsen Par Bjelkmar
Christian Blau Viacheslav Bolnykh Kevin Boyd
Aldert van Buuren Rudi van Drunen Anton Feenstra
Gilles Gouaillardet Alan Gray Gerrit Groenhof
Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
Aleksei Iupinov Christoph Junghans Joe Jordan
Dimitrios Karkoulis Peter Kasson Jiri Kraus
Carsten Kutzner Per Larsson Justin A. Lemkul
Viveca Lindahl Magnus Lundborg Erik Marklund
Pascal Merz Pieter Meulenhoff Teemu Murtola
Szilard Pall Sander Pronk Roland Schulz
Michael Shirts Alexey Shvetsov Alfons Sijbers
Peter Tieleman Jon Vincent Teemu Virolainen
Christian Wennberg Maarten Wolf Artem Zhmurov
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2019, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS: gmx editconf, version 2021
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /content
Command line:
gmx editconf -f complex.gro -o newbox.gro -bt dodecahedron -d 1.0
Note that major changes are planned in future for editconf, to improve usability and utility.
WARNING: Bad box in file complex.gro
Generated a cubic box 4.069 x 4.192 x 5.073
Read 2636 atoms
Volume: 86.5314 nm^3, corresponds to roughly 38900 electrons
No velocities found
system size : 4.069 4.192 5.073 (nm)
diameter : 5.849 (nm)
center : 2.241 -1.669 -0.935 (nm)
box vectors : 4.069 4.192 5.073 (nm)
box angles : 90.00 90.00 90.00 (degrees)
box volume : 86.53 (nm^3)
shift : 3.646 7.556 3.710 (nm)
new center : 5.887 5.887 2.775 (nm)
new box vectors : 7.849 7.849 7.849 (nm)
new box angles : 60.00 60.00 90.00 (degrees)
new box volume : 341.95 (nm^3)
GROMACS reminds you: "Why Do *You* Use Constraints ?" (H.J.C. Berendsen)
After this, there shouldn't be any change in the topology file, since there is only a "box" was added to the gro file
There should be a newbox.gro files was written as an output.
In [ ]:
!tail topol.top
#include "./charmm36-mar2019.ff/ions.itp" [ system ] ; Name LYSOZYME [ molecules ] ; Compound #mols Protein_chain_A 1 JZ4 1
In [ ]:
!/usr/local/gromacs/bin/gmx solvate -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro
:-) GROMACS - gmx solvate, 2021 (-:
GROMACS is written by:
Andrey Alekseenko Emile Apol Rossen Apostolov
Paul Bauer Herman J.C. Berendsen Par Bjelkmar
Christian Blau Viacheslav Bolnykh Kevin Boyd
Aldert van Buuren Rudi van Drunen Anton Feenstra
Gilles Gouaillardet Alan Gray Gerrit Groenhof
Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
Aleksei Iupinov Christoph Junghans Joe Jordan
Dimitrios Karkoulis Peter Kasson Jiri Kraus
Carsten Kutzner Per Larsson Justin A. Lemkul
Viveca Lindahl Magnus Lundborg Erik Marklund
Pascal Merz Pieter Meulenhoff Teemu Murtola
Szilard Pall Sander Pronk Roland Schulz
Michael Shirts Alexey Shvetsov Alfons Sijbers
Peter Tieleman Jon Vincent Teemu Virolainen
Christian Wennberg Maarten Wolf Artem Zhmurov
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2019, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS: gmx solvate, version 2021
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /content
Command line:
gmx solvate -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro
Reading solute configuration
Reading solvent configuration
Initialising inter-atomic distances...
WARNING: Masses and atomic (Van der Waals) radii will be guessed
based on residue and atom names, since they could not be
definitively assigned from the information in your input
files. These guessed numbers might deviate from the mass
and radius of the atom type. Please check the output
files if necessary.
NOTE: From version 5.0 gmx solvate uses the Van der Waals radii
from the source below. This means the results may be different
compared to previous GROMACS versions.
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
A. Bondi
van der Waals Volumes and Radii
J. Phys. Chem. 68 (1964) pp. 441-451
-------- -------- --- Thank You --- -------- --------
Generating solvent configuration
Will generate new solvent configuration of 5x5x3 boxes
Solvent box contains 37314 atoms in 12438 residues
Removed 3990 solvent atoms due to solvent-solvent overlap
Removed 2442 solvent atoms due to solute-solvent overlap
Sorting configuration
Found 1 molecule type:
SOL ( 3 atoms): 10294 residues
Generated solvent containing 30882 atoms in 10294 residues
Writing generated configuration to solv.gro
Output configuration contains 33518 atoms in 10458 residues
Volume : 341.949 (nm^3)
Density : 997.43 (g/l)
Number of solvent molecules: 10294
Processing topology
Adding line for 10294 solvent molecules with resname (SOL) to topology file (topol.top)
Back Off! I just backed up topol.top to ./#topol.top.1#
GROMACS reminds you: "I think everybody should like everybody." (Andy Warhol)
In [ ]:
!tail topol.top
[ system ] ; Name LYSOZYME in water [ molecules ] ; Compound #mols Protein_chain_A 1 JZ4 1 SOL 10294
Now you should see 10294 waters added to the topology,
In [ ]:
!wget http://www.mdtutorials.com/gmx/complex/Files/ions.mdp
--2021-06-10 08:04:05-- http://www.mdtutorials.com/gmx/complex/Files/ions.mdp Resolving www.mdtutorials.com (www.mdtutorials.com)... 13.59.3.21 Connecting to www.mdtutorials.com (www.mdtutorials.com)|13.59.3.21|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 1039 (1.0K) Saving to: ‘ions.mdp’ ions.mdp 100%[===================>] 1.01K --.-KB/s in 0s 2021-06-10 08:04:05 (156 MB/s) - ‘ions.mdp’ saved [1039/1039]
In [ ]:
!/usr/local/gromacs/bin/gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
:-) GROMACS - gmx grompp, 2021 (-:
GROMACS is written by:
Andrey Alekseenko Emile Apol Rossen Apostolov
Paul Bauer Herman J.C. Berendsen Par Bjelkmar
Christian Blau Viacheslav Bolnykh Kevin Boyd
Aldert van Buuren Rudi van Drunen Anton Feenstra
Gilles Gouaillardet Alan Gray Gerrit Groenhof
Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
Aleksei Iupinov Christoph Junghans Joe Jordan
Dimitrios Karkoulis Peter Kasson Jiri Kraus
Carsten Kutzner Per Larsson Justin A. Lemkul
Viveca Lindahl Magnus Lundborg Erik Marklund
Pascal Merz Pieter Meulenhoff Teemu Murtola
Szilard Pall Sander Pronk Roland Schulz
Michael Shirts Alexey Shvetsov Alfons Sijbers
Peter Tieleman Jon Vincent Teemu Virolainen
Christian Wennberg Maarten Wolf Artem Zhmurov
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2019, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS: gmx grompp, version 2021
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /content
Command line:
gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'ns_type'
NOTE 1 [file ions.mdp]:
With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
that with the Verlet scheme, nstlist has no effect on the accuracy of
your simulation.
Setting the LD random seed to -875233289
Generated 100032 of the 100128 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 65937 of the 100128 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
Excluding 3 bonded neighbours molecule type 'JZ4'
Excluding 2 bonded neighbours molecule type 'SOL'
NOTE 2 [file topol.top, line 24630]:
System has non-zero total charge: 6.000000
Total charge should normally be an integer. See
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
for discussion on how close it should be to an integer.
Analysing residue names:
There are: 163 Protein residues
There are: 1 Other residues
There are: 10294 Water residues
Analysing Protein...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Number of degrees of freedom in T-Coupling group rest is 69669.00
NOTE 3 [file ions.mdp]:
You are using a plain Coulomb cut-off, which might produce artifacts.
You might want to consider using PME electrostatics.
This run will generate roughly 3 Mb of data
There were 3 notes
GROMACS reminds you: "I'm An Oakman" (Pulp Fiction)
If you encounter an error here saying that you have different atom numbers in gro and top file, open the topol.top file to see if the JZ4 molecule type had bee actually added to the last block of the top file.
please select group 15:SOL for the next command
In [ ]:
!/usr/local/gromacs/bin/gmx genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL -neutral
:-) GROMACS - gmx genion, 2021 (-:
GROMACS is written by:
Andrey Alekseenko Emile Apol Rossen Apostolov
Paul Bauer Herman J.C. Berendsen Par Bjelkmar
Christian Blau Viacheslav Bolnykh Kevin Boyd
Aldert van Buuren Rudi van Drunen Anton Feenstra
Gilles Gouaillardet Alan Gray Gerrit Groenhof
Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
Aleksei Iupinov Christoph Junghans Joe Jordan
Dimitrios Karkoulis Peter Kasson Jiri Kraus
Carsten Kutzner Per Larsson Justin A. Lemkul
Viveca Lindahl Magnus Lundborg Erik Marklund
Pascal Merz Pieter Meulenhoff Teemu Murtola
Szilard Pall Sander Pronk Roland Schulz
Michael Shirts Alexey Shvetsov Alfons Sijbers
Peter Tieleman Jon Vincent Teemu Virolainen
Christian Wennberg Maarten Wolf Artem Zhmurov
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2019, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS: gmx genion, version 2021
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /content
Command line:
gmx genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL -neutral
Reading file ions.tpr, VERSION 2021 (single precision)
Reading file ions.tpr, VERSION 2021 (single precision)
Will try to add 0 NA ions and 6 CL ions.
Select a continuous group of solvent molecules
Group 0 ( System) has 33518 elements
Group 1 ( Protein) has 2614 elements
Group 2 ( Protein-H) has 1301 elements
Group 3 ( C-alpha) has 163 elements
Group 4 ( Backbone) has 489 elements
Group 5 ( MainChain) has 651 elements
Group 6 ( MainChain+Cb) has 803 elements
Group 7 ( MainChain+H) has 813 elements
Group 8 ( SideChain) has 1801 elements
Group 9 ( SideChain-H) has 650 elements
Group 10 ( Prot-Masses) has 2614 elements
Group 11 ( non-Protein) has 30904 elements
Group 12 ( Other) has 22 elements
Group 13 ( JZ4) has 22 elements
Group 14 ( Water) has 30882 elements
Group 15 ( SOL) has 30882 elements
Group 16 ( non-Water) has 2636 elements
Select a group: 15
Selected 15: 'SOL'
Number of (3-atomic) solvent molecules: 10294
Processing topology
Replacing 6 solute molecules in topology file (topol.top) by 0 NA and 6 CL ions.
Back Off! I just backed up topol.top to ./#topol.top.2#
Using random seed -1346398594.
Replacing solvent molecule 8537 (atom 28247) with CL
Replacing solvent molecule 9365 (atom 30731) with CL
Replacing solvent molecule 853 (atom 5195) with CL
Replacing solvent molecule 5898 (atom 20330) with CL
Replacing solvent molecule 6370 (atom 21746) with CL
Replacing solvent molecule 3206 (atom 12254) with CL
GROMACS reminds you: "What Kind Of Guru are You, Anyway ?" (F. Zappa)
In [ ]:
!tail topol.top
[ system ] ; Name LYSOZYME in water [ molecules ] ; Compound #mols Protein_chain_A 1 JZ4 1 SOL 10288 CL 6
Now you should see the solvent have decreased a little bit and 6 more chloride ions added instead
In [ ]:
!wget http://www.mdtutorials.com/gmx/complex/Files/em.mdp
!/usr/local/gromacs/bin/gmx grompp -f em.mdp -c solv_ions.gro -p topol.top -o em.tpr
!/usr/local/gromacs/bin/gmx mdrun -v -deffnm em
--2021-06-10 08:04:44-- http://www.mdtutorials.com/gmx/complex/Files/em.mdp
Resolving www.mdtutorials.com (www.mdtutorials.com)... 13.59.3.21
Connecting to www.mdtutorials.com (www.mdtutorials.com)|13.59.3.21|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 1168 (1.1K)
Saving to: ‘em.mdp’
em.mdp 100%[===================>] 1.14K --.-KB/s in 0s
2021-06-10 08:04:44 (175 MB/s) - ‘em.mdp’ saved [1168/1168]
:-) GROMACS - gmx grompp, 2021 (-:
GROMACS is written by:
Andrey Alekseenko Emile Apol Rossen Apostolov
Paul Bauer Herman J.C. Berendsen Par Bjelkmar
Christian Blau Viacheslav Bolnykh Kevin Boyd
Aldert van Buuren Rudi van Drunen Anton Feenstra
Gilles Gouaillardet Alan Gray Gerrit Groenhof
Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
Aleksei Iupinov Christoph Junghans Joe Jordan
Dimitrios Karkoulis Peter Kasson Jiri Kraus
Carsten Kutzner Per Larsson Justin A. Lemkul
Viveca Lindahl Magnus Lundborg Erik Marklund
Pascal Merz Pieter Meulenhoff Teemu Murtola
Szilard Pall Sander Pronk Roland Schulz
Michael Shirts Alexey Shvetsov Alfons Sijbers
Peter Tieleman Jon Vincent Teemu Virolainen
Christian Wennberg Maarten Wolf Artem Zhmurov
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2019, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS: gmx grompp, version 2021
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /content
Command line:
gmx grompp -f em.mdp -c solv_ions.gro -p topol.top -o em.tpr
Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'ns_type'
NOTE 1 [file em.mdp]:
With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
that with the Verlet scheme, nstlist has no effect on the accuracy of
your simulation.
Setting the LD random seed to -34637833
Generated 100032 of the 100128 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 65937 of the 100128 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
Excluding 3 bonded neighbours molecule type 'JZ4'
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 1 bonded neighbours molecule type 'CL'
Analysing residue names:
There are: 163 Protein residues
There are: 1 Other residues
There are: 10288 Water residues
There are: 6 Ion residues
Analysing Protein...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Number of degrees of freedom in T-Coupling group rest is 69651.00
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 72x72x72, spacing 0.109 0.109 0.109
Estimate for the relative computational load of the PME mesh part: 0.21
This run will generate roughly 3 Mb of data
There was 1 note
GROMACS reminds you: "I will not be a lemming and follow the crowd over the cliff and into the C." (John Beidler)
:-) GROMACS - gmx mdrun, 2021 (-:
GROMACS is written by:
Andrey Alekseenko Emile Apol Rossen Apostolov
Paul Bauer Herman J.C. Berendsen Par Bjelkmar
Christian Blau Viacheslav Bolnykh Kevin Boyd
Aldert van Buuren Rudi van Drunen Anton Feenstra
Gilles Gouaillardet Alan Gray Gerrit Groenhof
Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
Aleksei Iupinov Christoph Junghans Joe Jordan
Dimitrios Karkoulis Peter Kasson Jiri Kraus
Carsten Kutzner Per Larsson Justin A. Lemkul
Viveca Lindahl Magnus Lundborg Erik Marklund
Pascal Merz Pieter Meulenhoff Teemu Murtola
Szilard Pall Sander Pronk Roland Schulz
Michael Shirts Alexey Shvetsov Alfons Sijbers
Peter Tieleman Jon Vincent Teemu Virolainen
Christian Wennberg Maarten Wolf Artem Zhmurov
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2019, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS: gmx mdrun, version 2021
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /content
Command line:
gmx mdrun -v -deffnm em
Reading file em.tpr, VERSION 2021 (single precision)
1 GPU selected for this run.
Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:
PP:0
PP tasks will do (non-perturbed) short-ranged interactions on the GPU
PP task will update and constrain coordinates on the CPU
Using 1 MPI thread
Using 2 OpenMP threads
Steepest Descents:
Tolerance (Fmax) = 1.00000e+03
Number of steps = 50000
Step= 0, Dmax= 1.0e-02 nm, Epot= -2.46261e+05 Fmax= 1.58384e+05, atom= 784
Step= 1, Dmax= 1.0e-02 nm, Epot= -2.79766e+05 Fmax= 5.98207e+04, atom= 31116
Step= 2, Dmax= 1.2e-02 nm, Epot= -3.18296e+05 Fmax= 2.97398e+04, atom= 136
Step= 3, Dmax= 1.4e-02 nm, Epot= -3.49011e+05 Fmax= 1.72596e+04, atom= 24522
Step= 4, Dmax= 1.7e-02 nm, Epot= -3.72152e+05 Fmax= 2.08642e+04, atom= 24522
Step= 5, Dmax= 2.1e-02 nm, Epot= -3.82622e+05 Fmax= 2.31351e+04, atom= 24522
Step= 6, Dmax= 2.5e-02 nm, Epot= -3.90327e+05 Fmax= 1.44280e+04, atom= 24522
Step= 7, Dmax= 3.0e-02 nm, Epot= -4.00340e+05 Fmax= 3.14636e+04, atom= 24522
Step= 8, Dmax= 3.6e-02 nm, Epot= -4.04584e+05 Fmax= 1.38102e+04, atom= 490
Step= 9, Dmax= 4.3e-02 nm, Epot= -4.12204e+05 Fmax= 7.78076e+04, atom= 490
Step= 10, Dmax= 5.2e-02 nm, Epot= -4.15047e+05 Fmax= 1.12244e+04, atom= 490
Step= 11, Dmax= 6.2e-02 nm, Epot= -4.24133e+05 Fmax= 6.29234e+04, atom= 490
Step= 12, Dmax= 7.4e-02 nm, Epot= -4.26943e+05 Fmax= 1.39212e+04, atom= 134
Step= 14, Dmax= 4.5e-02 nm, Epot= -4.30823e+05 Fmax= 2.06113e+04, atom= 134
Step= 15, Dmax= 5.3e-02 nm, Epot= -4.33965e+05 Fmax= 1.69660e+04, atom= 134
Step= 16, Dmax= 6.4e-02 nm, Epot= -4.35494e+05 Fmax= 3.22387e+04, atom= 134
Step= 17, Dmax= 7.7e-02 nm, Epot= -4.36766e+05 Fmax= 4.89664e+04, atom= 137
Step= 18, Dmax= 9.2e-02 nm, Epot= -4.37856e+05 Fmax= 4.19492e+04, atom= 137
Step= 20, Dmax= 5.5e-02 nm, Epot= -4.41897e+05 Fmax= 1.68440e+04, atom= 139
Step= 23, Dmax= 1.7e-02 nm, Epot= -4.43852e+05 Fmax= 4.51501e+03, atom= 812
Step= 24, Dmax= 2.0e-02 nm, Epot= -4.44756e+05 Fmax= 2.17274e+04, atom= 812
Step= 25, Dmax= 2.4e-02 nm, Epot= -4.47423e+05 Fmax= 1.07332e+04, atom= 812
Step= 27, Dmax= 1.4e-02 nm, Epot= -4.48496e+05 Fmax= 8.53698e+03, atom= 812
Step= 28, Dmax= 1.7e-02 nm, Epot= -4.49030e+05 Fmax= 1.50747e+04, atom= 812
Step= 29, Dmax= 2.1e-02 nm, Epot= -4.50151e+05 Fmax= 1.27700e+04, atom= 812
Step= 31, Dmax= 1.2e-02 nm, Epot= -4.51450e+05 Fmax= 4.10216e+03, atom= 812
Step= 32, Dmax= 1.5e-02 nm, Epot= -4.52347e+05 Fmax= 1.55270e+04, atom= 812
Step= 33, Dmax= 1.8e-02 nm, Epot= -4.53805e+05 Fmax= 8.73350e+03, atom= 812
Step= 35, Dmax= 1.1e-02 nm, Epot= -4.54656e+05 Fmax= 5.63254e+03, atom= 812
Step= 36, Dmax= 1.3e-02 nm, Epot= -4.55219e+05 Fmax= 1.20417e+04, atom= 812
Step= 37, Dmax= 1.5e-02 nm, Epot= -4.56181e+05 Fmax= 8.71131e+03, atom= 812
Step= 39, Dmax= 9.3e-03 nm, Epot= -4.57019e+05 Fmax= 4.00326e+03, atom= 27
Step= 40, Dmax= 1.1e-02 nm, Epot= -4.57748e+05 Fmax= 1.11712e+04, atom= 27
Step= 41, Dmax= 1.3e-02 nm, Epot= -4.58663e+05 Fmax= 7.14866e+03, atom= 27
Step= 42, Dmax= 1.6e-02 nm, Epot= -4.58850e+05 Fmax= 1.48074e+04, atom= 27
Step= 43, Dmax= 1.9e-02 nm, Epot= -4.59816e+05 Fmax= 1.15257e+04, atom= 27
Step= 45, Dmax= 1.2e-02 nm, Epot= -4.60743e+05 Fmax= 4.17096e+03, atom= 27
Step= 46, Dmax= 1.4e-02 nm, Epot= -4.61186e+05 Fmax= 1.47916e+04, atom= 27
Step= 47, Dmax= 1.7e-02 nm, Epot= -4.62301e+05 Fmax= 7.85022e+03, atom= 27
Step= 49, Dmax= 1.0e-02 nm, Epot= -4.62900e+05 Fmax= 5.82365e+03, atom= 27
Step= 50, Dmax= 1.2e-02 nm, Epot= -4.63342e+05 Fmax= 1.05027e+04, atom= 27
Step= 51, Dmax= 1.4e-02 nm, Epot= -4.63943e+05 Fmax= 9.14724e+03, atom= 27
Step= 52, Dmax= 1.7e-02 nm, Epot= -4.64120e+05 Fmax= 1.44343e+04, atom= 27
Step= 53, Dmax= 2.1e-02 nm, Epot= -4.64687e+05 Fmax= 1.38094e+04, atom= 27
Step= 55, Dmax= 1.2e-02 nm, Epot= -4.65676e+05 Fmax= 3.03522e+03, atom= 27
Step= 56, Dmax= 1.5e-02 nm, Epot= -4.66144e+05 Fmax= 1.73722e+04, atom= 27
Step= 57, Dmax= 1.8e-02 nm, Epot= -4.67427e+05 Fmax= 6.93617e+03, atom= 27
Step= 59, Dmax= 1.1e-02 nm, Epot= -4.67853e+05 Fmax= 7.72795e+03, atom= 27
Step= 60, Dmax= 1.3e-02 nm, Epot= -4.68207e+05 Fmax= 9.82523e+03, atom= 27
Step= 61, Dmax= 1.5e-02 nm, Epot= -4.68555e+05 Fmax= 1.12505e+04, atom= 27
Step= 62, Dmax= 1.9e-02 nm, Epot= -4.68767e+05 Fmax= 1.40769e+04, atom= 27
Step= 63, Dmax= 2.2e-02 nm, Epot= -4.68970e+05 Fmax= 1.62171e+04, atom= 27
Step= 65, Dmax= 1.3e-02 nm, Epot= -4.70137e+05 Fmax= 1.86020e+03, atom= 27
Step= 66, Dmax= 1.6e-02 nm, Epot= -4.70827e+05 Fmax= 2.02052e+04, atom= 27
Step= 67, Dmax= 1.9e-02 nm, Epot= -4.72506e+05 Fmax= 5.91140e+03, atom= 27
Step= 69, Dmax= 1.2e-02 nm, Epot= -4.72728e+05 Fmax= 9.78909e+03, atom= 27
Step= 70, Dmax= 1.4e-02 nm, Epot= -4.73113e+05 Fmax= 9.08386e+03, atom= 27
Step= 71, Dmax= 1.7e-02 nm, Epot= -4.73132e+05 Fmax= 1.35109e+04, atom= 27
Step= 72, Dmax= 2.0e-02 nm, Epot= -4.73449e+05 Fmax= 1.36930e+04, atom= 27
Step= 74, Dmax= 1.2e-02 nm, Epot= -4.74363e+05 Fmax= 2.70598e+03, atom= 27
Step= 75, Dmax= 1.4e-02 nm, Epot= -4.74499e+05 Fmax= 1.68488e+04, atom= 27
Step= 76, Dmax= 1.7e-02 nm, Epot= -4.75595e+05 Fmax= 6.75129e+03, atom= 27
Step= 78, Dmax= 1.0e-02 nm, Epot= -4.75881e+05 Fmax= 7.33716e+03, atom= 27
Step= 79, Dmax= 1.2e-02 nm, Epot= -4.76089e+05 Fmax= 9.58385e+03, atom= 27
Step= 80, Dmax= 1.5e-02 nm, Epot= -4.76317e+05 Fmax= 1.07301e+04, atom= 27
Step= 81, Dmax= 1.8e-02 nm, Epot= -4.76393e+05 Fmax= 1.35848e+04, atom= 27
Step= 82, Dmax= 2.1e-02 nm, Epot= -4.76484e+05 Fmax= 1.56977e+04, atom= 27
Step= 84, Dmax= 1.3e-02 nm, Epot= -4.77499e+05 Fmax= 1.95919e+03, atom= 27
Step= 85, Dmax= 1.5e-02 nm, Epot= -4.77821e+05 Fmax= 1.90002e+04, atom= 27
Step= 86, Dmax= 1.8e-02 nm, Epot= -4.79019e+05 Fmax= 6.40174e+03, atom= 27
Step= 88, Dmax= 1.1e-02 nm, Epot= -4.79209e+05 Fmax= 8.78636e+03, atom= 27
Step= 89, Dmax= 1.3e-02 nm, Epot= -4.79433e+05 Fmax= 9.39615e+03, atom= 27
Step= 90, Dmax= 1.6e-02 nm, Epot= -4.79514e+05 Fmax= 1.24772e+04, atom= 27
Step= 91, Dmax= 1.9e-02 nm, Epot= -4.79665e+05 Fmax= 1.36624e+04, atom= 27
Step= 93, Dmax= 1.1e-02 nm, Epot= -4.80375e+05 Fmax= 1.95300e+03, atom= 27
Step= 94, Dmax= 1.4e-02 nm, Epot= -4.80541e+05 Fmax= 1.69441e+04, atom= 27
Step= 95, Dmax= 1.7e-02 nm, Epot= -4.81568e+05 Fmax= 5.58491e+03, atom= 27
Step= 97, Dmax= 9.9e-03 nm, Epot= -4.81721e+05 Fmax= 7.96273e+03, atom= 27
Step= 98, Dmax= 1.2e-02 nm, Epot= -4.81923e+05 Fmax= 8.31688e+03, atom= 27
Step= 99, Dmax= 1.4e-02 nm, Epot= -4.81967e+05 Fmax= 1.11764e+04, atom= 27
Step= 100, Dmax= 1.7e-02 nm, Epot= -4.82092e+05 Fmax= 1.22922e+04, atom= 27
Step= 102, Dmax= 1.0e-02 nm, Epot= -4.82768e+05 Fmax= 1.84285e+03, atom= 27
Step= 103, Dmax= 1.2e-02 nm, Epot= -4.82910e+05 Fmax= 1.50120e+04, atom= 27
Step= 104, Dmax= 1.5e-02 nm, Epot= -4.83767e+05 Fmax= 5.33300e+03, atom= 27
Step= 106, Dmax= 8.9e-03 nm, Epot= -4.83926e+05 Fmax= 6.83698e+03, atom= 27
Step= 107, Dmax= 1.1e-02 nm, Epot= -4.84085e+05 Fmax= 7.74902e+03, atom= 27
Step= 108, Dmax= 1.3e-02 nm, Epot= -4.84170e+05 Fmax= 9.78615e+03, atom= 27
Step= 109, Dmax= 1.5e-02 nm, Epot= -4.84257e+05 Fmax= 1.11879e+04, atom= 27
Step= 111, Dmax= 9.2e-03 nm, Epot= -4.84834e+05 Fmax= 1.35374e+03, atom= 27
Step= 112, Dmax= 1.1e-02 nm, Epot= -4.85058e+05 Fmax= 1.38126e+04, atom= 27
Step= 113, Dmax= 1.3e-02 nm, Epot= -4.85918e+05 Fmax= 4.27743e+03, atom= 27
Step= 115, Dmax= 8.0e-03 nm, Epot= -4.86026e+05 Fmax= 6.58527e+03, atom= 27
Step= 116, Dmax= 9.6e-03 nm, Epot= -4.86203e+05 Fmax= 6.48075e+03, atom= 27
Step= 117, Dmax= 1.1e-02 nm, Epot= -4.86206e+05 Fmax= 9.15884e+03, atom= 27
Step= 118, Dmax= 1.4e-02 nm, Epot= -4.86330e+05 Fmax= 9.66979e+03, atom= 27
Step= 120, Dmax= 8.3e-03 nm, Epot= -4.86872e+05 Fmax= 1.65682e+03, atom= 27
Step= 122, Dmax= 5.0e-03 nm, Epot= -4.87101e+05 Fmax= 5.08968e+03, atom= 27
Step= 123, Dmax= 6.0e-03 nm, Epot= -4.87315e+05 Fmax= 3.05210e+03, atom= 27
Step= 124, Dmax= 7.1e-03 nm, Epot= -4.87394e+05 Fmax= 6.71422e+03, atom= 27
Step= 125, Dmax= 8.6e-03 nm, Epot= -4.87635e+05 Fmax= 4.99671e+03, atom= 27
Step= 127, Dmax= 5.1e-03 nm, Epot= -4.87857e+05 Fmax= 2.01396e+03, atom= 27
Step= 128, Dmax= 6.2e-03 nm, Epot= -4.87985e+05 Fmax= 6.40815e+03, atom= 27
Step= 129, Dmax= 7.4e-03 nm, Epot= -4.88259e+05 Fmax= 3.69507e+03, atom= 27
Step= 131, Dmax= 4.4e-03 nm, Epot= -4.88432e+05 Fmax= 2.37730e+03, atom= 27
Step= 132, Dmax= 5.3e-03 nm, Epot= -4.88559e+05 Fmax= 4.90667e+03, atom= 27
Step= 133, Dmax= 6.4e-03 nm, Epot= -4.88749e+05 Fmax= 3.83056e+03, atom= 27
Step= 134, Dmax= 7.7e-03 nm, Epot= -4.88773e+05 Fmax= 6.67108e+03, atom= 27
Step= 135, Dmax= 9.2e-03 nm, Epot= -4.88968e+05 Fmax= 5.90346e+03, atom= 27
Step= 137, Dmax= 5.5e-03 nm, Epot= -4.89262e+05 Fmax= 1.62943e+03, atom= 27
Step= 138, Dmax= 6.6e-03 nm, Epot= -4.89319e+05 Fmax= 7.41446e+03, atom= 27
Step= 139, Dmax= 8.0e-03 nm, Epot= -4.89712e+05 Fmax= 3.44202e+03, atom= 27
Step= 141, Dmax= 4.8e-03 nm, Epot= -4.89862e+05 Fmax= 3.07797e+03, atom= 27
Step= 142, Dmax= 5.7e-03 nm, Epot= -4.89947e+05 Fmax= 4.75440e+03, atom= 27
Step= 143, Dmax= 6.9e-03 nm, Epot= -4.90089e+05 Fmax= 4.62958e+03, atom= 27
Step= 145, Dmax= 4.1e-03 nm, Epot= -4.90327e+05 Fmax= 9.95782e+02, atom= 27
writing lowest energy coordinates.
Steepest Descents converged to Fmax < 1000 in 146 steps
Potential Energy = -4.9032653e+05
Maximum force = 9.9578235e+02 on atom 27
Norm of force = 5.9065739e+01
GROMACS reminds you: "Bad times have a scientific value. These are occasions a good learner would not miss." (Ralph Waldo Emerson)
Make restrains¶
# Input this for the next command
> 0 & ! a H*
> qIn [ ]:
!/usr/local/gromacs/bin/gmx make_ndx -f jz4.gro -o index_jz4.ndx
:-) GROMACS - gmx make_ndx, 2021 (-:
GROMACS is written by:
Andrey Alekseenko Emile Apol Rossen Apostolov
Paul Bauer Herman J.C. Berendsen Par Bjelkmar
Christian Blau Viacheslav Bolnykh Kevin Boyd
Aldert van Buuren Rudi van Drunen Anton Feenstra
Gilles Gouaillardet Alan Gray Gerrit Groenhof
Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
Aleksei Iupinov Christoph Junghans Joe Jordan
Dimitrios Karkoulis Peter Kasson Jiri Kraus
Carsten Kutzner Per Larsson Justin A. Lemkul
Viveca Lindahl Magnus Lundborg Erik Marklund
Pascal Merz Pieter Meulenhoff Teemu Murtola
Szilard Pall Sander Pronk Roland Schulz
Michael Shirts Alexey Shvetsov Alfons Sijbers
Peter Tieleman Jon Vincent Teemu Virolainen
Christian Wennberg Maarten Wolf Artem Zhmurov
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2019, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS: gmx make_ndx, version 2021
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /content
Command line:
gmx make_ndx -f jz4.gro -o index_jz4.ndx
Reading structure file
Going to read 0 old index file(s)
Analysing residue names:
There are: 1 Other residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
0 System : 22 atoms
1 Other : 22 atoms
2 JZ4 : 22 atoms
nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups
'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues
't': atom type '|': or 'keep' nr 'splitat' nr 'h': help
'r': residue 'res' nr 'chain' char
"name": group 'case': case sensitive 'q': save and quit
'ri': residue index
> 0 & ! a H*
Copied index group 0 'System'
Found 12 atoms with name H*
Complemented group: 10 atoms
Merged two groups with AND: 22 10 -> 10
3 System_&_!H* : 10 atoms
> q
GROMACS reminds you: "You Can Be Too Early, You Can Be Too Late and You Can Be On Time" (J. Cruijff)
select "group 3" for the next command
In [ ]:
!/usr/local/gromacs/bin/gmx genrestr -f jz4.gro -n index_jz4.ndx -o posre_jz4.itp -fc 1000 1000 1000
:-) GROMACS - gmx genrestr, 2021 (-:
GROMACS is written by:
Andrey Alekseenko Emile Apol Rossen Apostolov
Paul Bauer Herman J.C. Berendsen Par Bjelkmar
Christian Blau Viacheslav Bolnykh Kevin Boyd
Aldert van Buuren Rudi van Drunen Anton Feenstra
Gilles Gouaillardet Alan Gray Gerrit Groenhof
Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
Aleksei Iupinov Christoph Junghans Joe Jordan
Dimitrios Karkoulis Peter Kasson Jiri Kraus
Carsten Kutzner Per Larsson Justin A. Lemkul
Viveca Lindahl Magnus Lundborg Erik Marklund
Pascal Merz Pieter Meulenhoff Teemu Murtola
Szilard Pall Sander Pronk Roland Schulz
Michael Shirts Alexey Shvetsov Alfons Sijbers
Peter Tieleman Jon Vincent Teemu Virolainen
Christian Wennberg Maarten Wolf Artem Zhmurov
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2019, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS: gmx genrestr, version 2021
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /content
Command line:
gmx genrestr -f jz4.gro -n index_jz4.ndx -o posre_jz4.itp -fc 1000 1000 1000
Reading structure file
Select group to position restrain
Group 0 ( System) has 22 elements
Group 1 ( Other) has 22 elements
Group 2 ( JZ4) has 22 elements
Group 3 ( System_&_!H*) has 10 elements
Select a group: 3
Selected 3: 'System_&_!H*'
GROMACS reminds you: "I always think there is something foreign about jolly phrases at breakfast." (Mr. Carson in Downtown Abbey)
next we need to modify the topology file again¶
In [ ]:
! cat topol.top > topol_2.txt
copy and pase this before "Include waters topology"
; Ligand position restraints
#ifdef POSRES
#include "posre_jz4.itp"
#endifI don't suggest you use next line command unless you know what it exactly will do, just copy and paste maybe.
In [ ]:
#!sed -i "/; Include water topology/ { N; s/; Include water topology\n/; Ligand position restraints ifdef POSRES include "posre_jz4.itp" endif\n&/ }" topol_2.txt
In [ ]:
!tail -30 topol_2.txt
#include "jz4.itp" ; Ligand position restraints # ifdef POSRES # include "posre_jz4.itp" # endif ; Include water topology #include "./charmm36-mar2019.ff/tip3p.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include topology for ions #include "./charmm36-mar2019.ff/ions.itp" [ system ] ; Name LYSOZYME in water [ molecules ] ; Compound #mols Protein_chain_A 1 JZ4 1 SOL 10288 CL 6
In [ ]:
!cat topol_2.txt > topol.top
Input this for the next command
> 1 | 13
> qIn [ ]:
!/usr/local/gromacs/bin/gmx make_ndx -f em.gro -o index.ndx
:-) GROMACS - gmx make_ndx, 2021 (-:
GROMACS is written by:
Andrey Alekseenko Emile Apol Rossen Apostolov
Paul Bauer Herman J.C. Berendsen Par Bjelkmar
Christian Blau Viacheslav Bolnykh Kevin Boyd
Aldert van Buuren Rudi van Drunen Anton Feenstra
Gilles Gouaillardet Alan Gray Gerrit Groenhof
Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
Aleksei Iupinov Christoph Junghans Joe Jordan
Dimitrios Karkoulis Peter Kasson Jiri Kraus
Carsten Kutzner Per Larsson Justin A. Lemkul
Viveca Lindahl Magnus Lundborg Erik Marklund
Pascal Merz Pieter Meulenhoff Teemu Murtola
Szilard Pall Sander Pronk Roland Schulz
Michael Shirts Alexey Shvetsov Alfons Sijbers
Peter Tieleman Jon Vincent Teemu Virolainen
Christian Wennberg Maarten Wolf Artem Zhmurov
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2019, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS: gmx make_ndx, version 2021
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /content
Command line:
gmx make_ndx -f em.gro -o index.ndx
Reading structure file
Going to read 0 old index file(s)
Analysing residue names:
There are: 163 Protein residues
There are: 1 Other residues
There are: 10288 Water residues
There are: 6 Ion residues
Analysing Protein...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
0 System : 33506 atoms
1 Protein : 2614 atoms
2 Protein-H : 1301 atoms
3 C-alpha : 163 atoms
4 Backbone : 489 atoms
5 MainChain : 651 atoms
6 MainChain+Cb : 803 atoms
7 MainChain+H : 813 atoms
8 SideChain : 1801 atoms
9 SideChain-H : 650 atoms
10 Prot-Masses : 2614 atoms
11 non-Protein : 30892 atoms
12 Other : 22 atoms
13 JZ4 : 22 atoms
14 CL : 6 atoms
15 Water : 30864 atoms
16 SOL : 30864 atoms
17 non-Water : 2642 atoms
18 Ion : 6 atoms
19 JZ4 : 22 atoms
20 CL : 6 atoms
21 Water_and_ions : 30870 atoms
nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups
'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues
't': atom type '|': or 'keep' nr 'splitat' nr 'h': help
'r': residue 'res' nr 'chain' char
"name": group 'case': case sensitive 'q': save and quit
'ri': residue index
> 1 | 13
Copied index group 1 'Protein'
Copied index group 13 'JZ4'
Merged two groups with OR: 2614 22 -> 2636
22 Protein_JZ4 : 2636 atoms
> q
GROMACS reminds you: "I invented the term 'Object-Oriented', and I can tell you I did not have C++ in mind." (Alan Kay, author of Smalltalk)
Part 2, from here we start prepare for Free energy pertubation, we will¶
get all calculations done in the "new" folder
From here, I will build a new folder called new, and two sub-folders called complex and solvent will be created as well
In [ ]:
%%bash
cd /content/
#mkdir new
cd new
#mkdir complex solvent
cd complex
Some necessary file, the first one is the run.sh which controls the whole calculation progress, from my blog . Just in case that if you read this after 2023, this link may failed due to a potential domain time limit of my personal website, in that case you may consider to contact me via my email at the very beginning of the notebook.
In [ ]:
!pwd
/content
In [ ]:
#https://drive.google.com/file/d/1ksNkv0pB7_U83tcgWA0etGVxJTdfINTL/view?usp=sharing
#!wget "https://drive.google.com/uc?export=download&id=1ksNkv0pB7_U83tcgWA0etGVxJTdfINTL"
#!git clone https://github.com/chentinghao/download_google_drive.git
#%cd download_google_drive/
#!python download_gdrive.py 1ksNkv0pB7_U83tcgWA0etGVxJTdfINTL run.sh # this string is from my drive file ID
#https://drive.google.com/file/d/1ioq0VIESqbi-K9cTxaqEJ9K7LoVPsPOQ/view?usp=sharing
!wget https://qutesun.ml/img/post18/run.sh
!cp run.sh /content/new/complex
--2021-06-10 08:11:29-- https://qutesun.ml/img/post18/run.sh Resolving qutesun.ml (qutesun.ml)... 76.76.21.21 Connecting to qutesun.ml (qutesun.ml)|76.76.21.21|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 1216 (1.2K) [application/x-sh] Saving to: ‘run.sh’ run.sh 100%[===================>] 1.19K --.-KB/s in 0s 2021-06-10 08:11:29 (21.2 MB/s) - ‘run.sh’ saved [1216/1216]
Now we will download the content of the Gromacs ABFE tutorial form http://www.alchemistry.org/wiki/ , we will utilize its simulation script with modification to adapt it to our protein 3htb, or potentially your protein of interest.
In [ ]:
%%bash
cd /content/
mkdir Gromacs_tutorial_files
cd Gromacs_tutorial_files
wget http://www.alchemistry.org/wiki/images/1/17/InputFiles_ABFE_GMX2016.zip
unzip InputFiles_ABFE_GMX2016.zip
Archive: InputFiles_ABFE_GMX2016.zip creating: InputFiles_ABFE_GMX2016/ inflating: InputFiles_ABFE_GMX2016/.DS_Store creating: __MACOSX/ creating: __MACOSX/InputFiles_ABFE_GMX2016/ inflating: __MACOSX/InputFiles_ABFE_GMX2016/._.DS_Store creating: InputFiles_ABFE_GMX2016/complex/ inflating: InputFiles_ABFE_GMX2016/complex/.DS_Store creating: __MACOSX/InputFiles_ABFE_GMX2016/complex/ inflating: __MACOSX/InputFiles_ABFE_GMX2016/complex/._.DS_Store inflating: InputFiles_ABFE_GMX2016/complex/complex.gro inflating: __MACOSX/InputFiles_ABFE_GMX2016/complex/._complex.gro inflating: InputFiles_ABFE_GMX2016/complex/complex.top inflating: __MACOSX/InputFiles_ABFE_GMX2016/complex/._complex.top creating: InputFiles_ABFE_GMX2016/complex/lambda.00/ inflating: __MACOSX/InputFiles_ABFE_GMX2016/complex/._lambda.00 creating: InputFiles_ABFE_GMX2016/complex/lambda.01/ inflating: __MACOSX/InputFiles_ABFE_GMX2016/complex/._lambda.01 creating: InputFiles_ABFE_GMX2016/complex/lambda.02/ inflating: __MACOSX/InputFiles_ABFE_GMX2016/complex/._lambda.02 creating: InputFiles_ABFE_GMX2016/complex/lambda.03/ inflating: __MACOSX/InputFiles_ABFE_GMX2016/complex/._lambda.03 creating: InputFiles_ABFE_GMX2016/complex/lambda.04/ inflating: __MACOSX/InputFiles_ABFE_GMX2016/complex/._lambda.04 creating: InputFiles_ABFE_GMX2016/complex/lambda.05/ inflating: __MACOSX/InputFiles_ABFE_GMX2016/complex/._lambda.05 creating: InputFiles_ABFE_GMX2016/complex/lambda.06/ inflating: __MACOSX/InputFiles_ABFE_GMX2016/complex/._lambda.06 creating: InputFiles_ABFE_GMX2016/complex/lambda.07/ inflating: __MACOSX/InputFiles_ABFE_GMX2016/complex/._lambda.07 creating: InputFiles_ABFE_GMX2016/complex/lambda.08/ inflating: __MACOSX/InputFiles_ABFE_GMX2016/complex/._lambda.08 creating: InputFiles_ABFE_GMX2016/complex/lambda.09/ inflating: __MACOSX/InputFiles_ABFE_GMX2016/complex/._lambda.09 creating: InputFiles_ABFE_GMX2016/complex/lambda.10/ inflating: __MACOSX/InputFiles_ABFE_GMX2016/complex/._lambda.10 creating: InputFiles_ABFE_GMX2016/complex/lambda.11/ inflating: __MACOSX/InputFiles_ABFE_GMX2016/complex/._lambda.11 creating: InputFiles_ABFE_GMX2016/complex/lambda.12/ inflating: __MACOSX/InputFiles_ABFE_GMX2016/complex/._lambda.12 creating: InputFiles_ABFE_GMX2016/complex/lambda.13/ inflating: __MACOSX/InputFiles_ABFE_GMX2016/complex/._lambda.13 creating: InputFiles_ABFE_GMX2016/complex/lambda.14/ inflating: __MACOSX/InputFiles_ABFE_GMX2016/complex/._lambda.14 creating: InputFiles_ABFE_GMX2016/complex/lambda.15/ inflating: __MACOSX/InputFiles_ABFE_GMX2016/complex/._lambda.15 creating: InputFiles_ABFE_GMX2016/complex/lambda.16/ inflating: __MACOSX/InputFiles_ABFE_GMX2016/complex/._lambda.16 creating: InputFiles_ABFE_GMX2016/complex/lambda.17/ inflating: __MACOSX/InputFiles_ABFE_GMX2016/complex/._lambda.17 creating: InputFiles_ABFE_GMX2016/complex/lambda.18/ inflating: __MACOSX/InputFiles_ABFE_GMX2016/complex/._lambda.18 creating: InputFiles_ABFE_GMX2016/complex/lambda.19/ inflating: 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InputFiles_ABFE_GMX2016/complex/lambda.28/ inflating: __MACOSX/InputFiles_ABFE_GMX2016/complex/._lambda.28 creating: InputFiles_ABFE_GMX2016/complex/lambda.29/ inflating: __MACOSX/InputFiles_ABFE_GMX2016/complex/._lambda.29 inflating: InputFiles_ABFE_GMX2016/complex/ligand.itp inflating: __MACOSX/InputFiles_ABFE_GMX2016/complex/._ligand.itp creating: InputFiles_ABFE_GMX2016/complex/MDP/ inflating: InputFiles_ABFE_GMX2016/complex/MDP/.DS_Store creating: __MACOSX/InputFiles_ABFE_GMX2016/complex/MDP/ inflating: __MACOSX/InputFiles_ABFE_GMX2016/complex/MDP/._.DS_Store creating: InputFiles_ABFE_GMX2016/complex/MDP/ENMIN/ inflating: InputFiles_ABFE_GMX2016/complex/MDP/ENMIN/enmin.00.mdp inflating: InputFiles_ABFE_GMX2016/complex/MDP/ENMIN/enmin.01.mdp inflating: InputFiles_ABFE_GMX2016/complex/MDP/ENMIN/enmin.02.mdp inflating: InputFiles_ABFE_GMX2016/complex/MDP/ENMIN/enmin.03.mdp inflating: InputFiles_ABFE_GMX2016/complex/MDP/ENMIN/enmin.04.mdp inflating: 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InputFiles_ABFE_GMX2016/complex/MDP/NPT/npt.19.mdp inflating: InputFiles_ABFE_GMX2016/complex/MDP/NPT/npt.20.mdp inflating: InputFiles_ABFE_GMX2016/complex/MDP/NPT/npt.21.mdp inflating: InputFiles_ABFE_GMX2016/complex/MDP/NPT/npt.22.mdp inflating: InputFiles_ABFE_GMX2016/complex/MDP/NPT/npt.23.mdp inflating: InputFiles_ABFE_GMX2016/complex/MDP/NPT/npt.24.mdp inflating: InputFiles_ABFE_GMX2016/complex/MDP/NPT/npt.25.mdp inflating: InputFiles_ABFE_GMX2016/complex/MDP/NPT/npt.26.mdp inflating: InputFiles_ABFE_GMX2016/complex/MDP/NPT/npt.27.mdp inflating: InputFiles_ABFE_GMX2016/complex/MDP/NPT/npt.28.mdp inflating: InputFiles_ABFE_GMX2016/complex/MDP/NPT/npt.29.mdp creating: InputFiles_ABFE_GMX2016/complex/MDP/NVT/ inflating: InputFiles_ABFE_GMX2016/complex/MDP/NVT/nvt.00.mdp inflating: InputFiles_ABFE_GMX2016/complex/MDP/NVT/nvt.01.mdp inflating: InputFiles_ABFE_GMX2016/complex/MDP/NVT/nvt.02.mdp inflating: InputFiles_ABFE_GMX2016/complex/MDP/NVT/nvt.03.mdp inflating: 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On the basis of our previous new folder which contains complex and solvent, we now need move further to build all the lambda folders the pertubation path rely on, but first let's coy the MDP folder from Alchemistry.org which contains all the simulation parameters, to our complex and solvent folder.
In [ ]:
%%bash
cd /content/new/complex/
cp -r /content/Gromacs_tutorial_files/InputFiles_ABFE_GMX2016/complex/MDP ./
cp -r /content/Gromacs_tutorial_files/InputFiles_ABFE_GMX2016/ligand/MDP ../solvent
cp run.sh ../solvent
Now you should have a MDP folder in both solvent and complex, with an run.sh in each folder as well. Next, time for making the lambda folders, the command is to make 30 lambda folder in complex, 20 in solvent. Note, you could decide to make both 30, or 30/40, it depends more on what kind of compute resources you have access to or how good you want your calculation would be, the more the better, but you also don't want it takes forever to finish.
In [ ]:
%%bash
cd /content/new/complex/
for (( a = 0; a <=2; a++ ));
do
for (( b = 0; b <10; b++ ))
do
mkdir lambda.$a.$b
done
done
In [ ]:
%%bash
cd /content/new/solvent/
for (( a = 0; a <=1; a++ ));
do
for (( b = 0; b <10; b++ ))
do
mkdir lambda.$a.$b
done
done
The reason the complex need a bit more lambda windows is that this branch need to deal with both protein and ligand, while for the solvent, there is only a liand need to be calculate.
Now time to copy all the files we have produced from Justin's tutorial to the new folder, where the FEP will happen.
In [ ]:
%%bash
cd /content/new/solvent/
cp /content/jz4.gro ./
cp /content/jz4.top ./
cp /content/posre_jz4.itp ./
cp /content/index_jz4.ndx ./
cp /content/jz4.prm ./
cp /content/jz4.itp ./
In [ ]:
%%bash
cd /content/new/solvent/
ls # check if all the files have been copied into solvent.
index_jz4.ndx jz4.gro jz4.itp jz4.prm jz4.top lambda.0.0 lambda.0.1 lambda.0.2 lambda.0.3 lambda.0.4 lambda.0.5 lambda.0.6 lambda.0.7 lambda.0.8 lambda.0.9 lambda.1.0 lambda.1.1 lambda.1.2 lambda.1.3 lambda.1.4 lambda.1.5 lambda.1.6 lambda.1.7 lambda.1.8 lambda.1.9 MDP posre_jz4.itp run.sh
In [ ]:
%%bash
cd /content/new/complex/
cp /content/solv_ions.gro ./
cp /content/topol.top ./
cp /content/index.ndx ./
cp /content/posre.itp ./
cp /content/jz4.gro ./
cp /content/jz4.top ./
cp /content/posre_jz4.itp ./
cp /content/index_jz4.ndx ./
cp /content/jz4.prm ./
cp /content/jz4.itp ./
In [ ]:
%%bash
cd /content/new/complex/
ls #double check if all files have been copied to the compelx folder
index_jz4.ndx index.ndx jz4.gro jz4.itp jz4.prm jz4.top lambda.0.0 lambda.0.1 lambda.0.2 lambda.0.3 lambda.0.4 lambda.0.5 lambda.0.6 lambda.0.7 lambda.0.8 lambda.0.9 lambda.1.0 lambda.1.1 lambda.1.2 lambda.1.3 lambda.1.4 lambda.1.5 lambda.1.6 lambda.1.7 lambda.1.8 lambda.1.9 lambda.2.0 lambda.2.1 lambda.2.2 lambda.2.3 lambda.2.4 lambda.2.5 lambda.2.6 lambda.2.7 lambda.2.8 lambda.2.9 MDP posre.itp posre_jz4.itp run.sh solv_ions.gro topol.top
What we have done, is , we have copied some input files generated from Justin's tutorial, but don't forget the simulation script is from Alchemistry.org, so there is a miss match and we need to fix it.
In [ ]:
%%bash
cd /content/new/complex/MDP/ENMIN/ # change the orignal "ligand" to "JZ4"
sed -i 's/ligand/JZ4/' *.mdp # ENMIN
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%%bash
cd /content/new/complex/MDP/NVT/ # NVT script modification，the origianl temperature control is by "system", here, we use a two-part system based on Justin's tutorial.
sed -i 's/ligand/JZ4/' *.mdp # the two-part system is " Protein_JZ4 and Water_and_ions" which we have produced from Justin's tutorial.
sed -i 's/System/Protein_JZ4 Water_and_ions/' *.mdp #NVT
sed -i 's/tau_t = 1.0/tau_t = 1.0 1.0/' *.mdp #NVT
sed -i 's/ef_t = 300/ef_t = 300 300/' *.mdp #NVT
#NPT :same as NVT
#PROT：same as NVT
In [ ]:
%%bash
cd /content/new/complex/MDP/NPT/ #
sed -i 's/ligand/JZ4/' *.mdp #NPT
sed -i 's/System/Protein_JZ4 Water_and_ions/' *.mdp #NPT
sed -i 's/tau_t = 1.0/tau_t = 1.0 1.0/' *.mdp #NPT
sed -i 's/ef_t = 300/ef_t = 300 300/' *.mdp #NPT
#PROT： 同上NVT
In [ ]:
%%bash
cd /content/new/complex/MDP/PROD//
sed -i 's/ligand/JZ4/' *.mdp #PROD
sed -i 's/System/Protein_JZ4 Water_and_ions/' *.mdp #PROD
sed -i 's/tau_t = 1.0/tau_t = 1.0 1.0/' *.mdp #PROD
sed -i 's/ef_t = 300/ef_t = 300 300/' *.mdp #PROD
we have downloaded a run.sh script previously, in that script I use for loop to control the FEP progress with two variables "a" and "b", to allow myself be able to apply this loop on a folder name, I have to change the folder name form ab to a.b, and that is also the way when we have created the 20 or 30 lambda folders but not the case for those folder from Alchemistry.org inside teh MDP folder. We need to change the folder name style a bit.
Change the lambda folder name style to be compatable with run.sh¶
In [ ]:
%%bash
cd /content/new/complex/MDP/ENMIN/
for (( a = 0; a <=2; a++ ))
do
for (( b = 0; b <=9; b++ ))
do
mv enmin.$a$b.mdp enmin.$a.$b.mdp
done
done
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%%bash
cd /content/new/complex/MDP/NVT/
for (( a = 0; a <=2; a++ ))
do
for (( b = 0; b <=9; b++ ))
do
mv nvt.$a$b.mdp nvt.$a.$b.mdp
done
done
In [ ]:
%%bash
cd /content/new/complex/MDP/NPT/
for (( a = 0; a <=2; a++ ))
do
for (( b = 0; b <=9; b++ ))
do
mv npt.$a$b.mdp npt.$a.$b.mdp
done
done
In [ ]:
%%bash
cd /content/new/complex/MDP/PROD/
for (( a = 0; a <=2; a++ ))
do
for (( b = 0; b <=9; b++ ))
do
mv prod.$a$b.mdp prod.$a.$b.mdp
done
done
You may want to have a look at if there has been one more dot added to the folders inside MDP.
Next, one more thins you could decide is to add the INTER molecular restrain or not, if you add it, the calculation logic will be better, and the result would be more convincing, but if you don't the calculation can also be done as well. The later choice is easier cause we don't have to calculate the one more number account for the inter molecular restrain inside the solvent branch.
In [ ]:
!cat topol.top > topol.txt
[ intermolecular_interactions]
[ bonds ]
; ai aj type bA kA bB kB
1391 2615 6 0.654 0.0 0.654 4184.0
[ angles ]
; ai aj ak type thA fcA thB fcB
1393 1391 2615 1 88.8 0.0 88.8 41.84
1391 2615 2614 1 32.9 0.0 32.9 41.84
[ dihedrals ]
; ai aj ak al type thA fcA thB fcB
1410 1393 1391 2615 2 -159.7 0.0 -159.7 41.84
1393 1391 2615 2614 2 122.6 0.0 122.6 41.84
1391 2615 2614 2610 2 12.8 0.0 12.8 41.84In [ ]:
!mv topol.txt topol.top
In [ ]:
%%bash
cd /content/new/complex/
cp -r /content/charmm36-mar2019.ff/ ./
Next is the run.sh time, there is an time limit of 12 hours from colab, so you may want to modify the a and b range to only calculate a small number of lambda folders.
For example, if I only want to do lambda.0.0 to lambda.0.5
for (( a = 0; a <=0; a++ ))
do
for (( b = 0; b <5; b++ ))
doIn [ ]:
%cd /content/new/complex
/content/new/complex
In [ ]:
!cp /content/topol.top ./
In [ ]:
%%bash
cd /content/new/complex ###please double check the command line differences in "complex" and "solvent"
for (( a = 0; a <=0; a++ ))
do
for (( b = 0; b <3; b++ ))
do
cd lambda.$a.$b
mkdir ENMIN
cd ENMIN
/usr/local/gromacs/bin/gmx grompp -f ../../MDP/ENMIN/enmin.$a.$b.mdp -c ../../solv_ions.gro -p ../../topol.top -n ../../index.ndx -o enmin.tpr
/usr/local/gromacs/bin/gmx mdrun -v -stepout 1000 -s enmin.tpr -deffnm enmin
cd ../
mkdir NVT
cd NVT
/usr/local/gromacs/bin/gmx grompp -f ../../MDP/NVT/nvt.$a.$b.mdp -c ../ENMIN/enmin.gro -p ../../topol.top -n ../../index.ndx -o nvt.tpr -r ../../solv_ions.gro
/usr/local/gromacs/bin/gmx mdrun -stepout 1000 -s nvt.tpr -deffnm nvt
cd ../
mkdir NPT
cd NPT
/usr/local/gromacs/bin/gmx grompp -f ../../MDP/NPT/npt.$a.$b.mdp -c ../NVT/nvt.gro -t ../NVT/nvt.cpt -p ../../topol.top -n ../../index.ndx -o npt.tpr -r ../../solv_ions.gro
/usr/local/gromacs/bin/gmx mdrun -stepout 1000 -s npt.tpr -deffnm npt
cd ../
mkdir PROD
cd PROD
/usr/local/gromacs/bin/gmx grompp -f ../../MDP/PROD/prod.$a.$b.mdp -c ../NPT/npt.gro -t ../NPT/npt.cpt -p ../../topol.top -n ../../index.ndx -o prod.tpr
/usr/local/gromacs/bin/gmx mdrun -stepout 1000 -s prod.tpr -deffnm prod -dhdl dhdl
cd ../../
done
done
In [ ]:
结果分析 (未完成，仍在编辑中)¶
In [ ]:
%cd /content/download_google_drive/
!python download_gdrive.py 1ioq0VIESqbi-K9cTxaqEJ9K7LoVPsPOQ cp_xvg.sh # 下载可以收集所有dhdl文件的脚本
#https://drive.google.com/file/d/1ioq0VIESqbi-K9cTxaqEJ9K7LoVPsPOQ/view?usp=sharing
In [ ]:
%%bash
cd /content/new/complex # 回到complex 界面，准备开始收集各个自文件夹lambda中的PROD 文件夹中的结果dhdl 文件
cp /content/download_google_drive/cp_xvg.sh ./
./cp_xvg.sh
# This is formatted as code # 这是收集dhdl 文件脚本的内部指令
#!/bin/bash
if [ ! -d "dHdl_files" ]; then
mkdir dHdl_files
fi
for i in $(ls | grep "lambda.*"); do
lam="${i##*.}"
cp ./$i/PROD/dhdl.xvg ./dHdl_files/dhdl.$lam.xvg
done接下来我们到含有所有dhdl 文件的文件夹内运行以下指令，来处理这些数据，拿到complex 这一支的能量变化，即下图中从F 到D的能量变化。为了更方便的分子这些数据，我们参考原始教程中的建议，即安装一个python 工具，来进行最后的计算
In [ ]:
!git clone https://github.com/MobleyLab/alchemical-analysis.git
%cd alchemical-analysis
!sudo python setup.py install
注意替换下面红色的路径为我们的含有dhdl文件的路径，替换红色的prefix 为 dhdl。 如果想完整了解代码的意义，请使用
alchemical_analysis.py -h调出所有的说明
In [ ]:
alchemical_analysis.py -d 'directory' -p 'prefix' -t 300 -s 100 -u kcal -w -g
接下来请前往Solvent 一支完成所有的计算，采用同样的方法分析数据，得到这一支的能量变化。¶
最后两支相加即为总的绝对结合自由能数值，这里暂时没有考虑分子间约束势的能量校正。¶
在运算的过程中，虽然没有使用我们本机的cpu， 但你仍需要保持计算窗口的打开；如果你有ipd, 也可考虑再ipd 上进行运行，保证ipad 电量充足，不关闭网页即可。