This blog provides two script to improve the default NAMD input configration file generated from Feprepare web server. It is good to use this blog with the blog written on 2nd December, 2020.
You could generate the "file.zip" from Feprepare web server based on your ligands of interest before using the scripts. Another two files are provided here for free downloading, all the extraction codes are 9999. One is the toppar file which contains all the topology files need for the simulation, the other is the parameter patch file .
After the three files ready, to use these two scripts, in the complex or solvent directory.(you need to modify the namd path to your NAMD installation location)
$ chmod +x complex-leg-patch.sh
$ ./complex-leg-patch.sh
complex-leg-patch.sh
#!/bin/bash
# This script is written for the purpose to do ligand mutation free energy perturbation.
# I assume you use the web server "Feprepare" to generate "all" necessary input files
# towards NAMD simulation. This script can help to change the "lambda by lambda"
# simulation sequence to "all lambda in one" simulation, making the simulation easier
# to handle and analysis later. The directory location to run this script should be
# the "complex" or "solvent", respectively. This one is for complex leg.
##email to quantaosun@gmail.com if there is any issues or errors.
# It should be advised; the author of this script only have preliminary knowledge of
# coding, so use this script at your own risk !
############ NVT script modification ##################################
cp conf_complex/nvt_equil.namd ./
head -n 13 nvt_equil.namd > output1
cat parameter_patch.txt >> output1
tail -n +14 nvt_equil.namd > output2
sed -i 's/ionized.fep/ionized_complex.fep/' output2
cat output2 >> output1
mv output1 nvt_equil_modi.namd
############ NPT script modification #####################################
cp conf_complex/npt_equil.namd ./
head -n 13 npt_equil.namd > output3
cat parameter_patch.txt >> output3
tail -n +14 npt_equil.namd > output4
sed -i 's/ionized.fep/ionized_complex.fep/' output4
cat output4 >> output3
mv output3 npt_equil_modi.namd
############### Production script modification #################################
cp conf_complex/md_forward_1.namd ./
tail -n 3 md_forward_1.namd > tmp2.txt
echo "alchEquilSteps 0
set numSteps 500000 ; # 0.5 ns as a total
runFEP 0.0 1.0 0.0625 $numSteps" > tmp2.txt # overwrite the original Lambda0 Lambda2 format, 16 lambda windows
cat tmp2.txt >> md_forward_1.namd
#To uncomment lines 139 through 141 to close the one by one simulation.
sed -i '139,141 s/^/#/' md_forward_1.namd #double check the line numbers.
head -n 123 md_forward_1.namd > outputA
tail -n +124 md_forward_1.namd > outputB
echo "source ../fep.tcl" >> outputA
cat outputB >> outputA
mv outputA md_forward_1.namd
#################### To substitute the alchFile ##############
head -n 13 md_forward_1.namd > output5
cat parameter_patch.txt >> output5
tail -n +14 md_forward_1.namd > output6
sed -i 's/ionized.fep/ionized_complex.fep/' output6 # correct the B column with -1
sed -i '/^alchDecouple/s/off/yes/' output6 # turn on the "alchDecouple"
cat output6 >> output5
mv output5 md_forward_modi.namd
########Running the job#################################
qsub -I -l select=1:ncpus=32:mem=40gb,walltime=10:00:00 -M your_email@.. -m aeb
cd $PBS_O_WORKDIR
module load intel/18.0.1.163 openmpi/3.1.2-intel namd/2.13-mpi
export Honey_NAMD=/apps/namd/2.13-mpi/arch/Linux-x86_64-icc # this need to be modified
###################################################################
mpirun --oversubscribe -np 4 $Fuck_NAMD/namd2 +ppn 7 nvt_equil_modi.namd > nvt_equil_modi.out
#NPT###############################################################
mpirun --oversubscribe -np 4 $Fuck_NAMD/namd2 +ppn 7 npt_equil_modi.namd > npt_equil_modi.out
# Production#######################################################
mpirun --oversubscribe -np 4 $Fuck_NAMD/namd2 +ppn 7 md_forward_modi.namd > md_forward_modi.out
solvent-leg-patch.sh
To use these two scripts, in the complex or solvent directory.
chmod +x solvent-leg-patch.sh
./solvent-leg-patch.sh
#!/bin/bash
# This script is written for the purpose to do ligand mutation free energy pertubation.
# I assume you use the web server "Feprepare" to generate "all" necessary input files
# towards NAMD simlation. This script can help to change the "lambda by lambda"
# simulation sequence to "all lambda in one" simulation, making the simulation easier
# to handle and analysis later. The directory location to run this script should be
# the "complex" or "solvent", respectively. This one is for solvent leg.
##email to quantaosun@gmail.com if there is any issues or errors.
# It should be advised; the author of this script only have preliminary knowledge of
# coding, so use this script at your own risk !
############ NVT script modification ##################################
cp conf_solvent/nvt_equil.namd ./
head -n 13 nvt_equil.namd > output1
cat parameter_patch.txt >> output1
tail -n +14 nvt_equil.namd > output2
sed -i 's/ionized.fep/ionized_solvent.fep/' output2
cat output2 >> output1
mv output1 nvt_equil_modi.namd
############ NPT script modification #####################################
cp conf_solvent/npt_equil.namd ./
head -n 13 npt_equil.namd > output3
cat parameter_patch.txt >> output3
tail -n +14 npt_equil.namd > output4
sed -i 's/ionized.fep/ionized_solvent.fep/' output4
cat output4 >> output3
mv output3 npt_equil_modi.namd
############### Production script modification #################################
cp conf_solvent/md_forward_1.namd ./
tail -n 3 md_forward_1.namd > tmp2.txt
echo "alchEquilSteps 0
set numSteps 500000 ; # 0.5 ns as a total
runFEP 0.0 1.0 0.0625 $numSteps" > tmp2.txt # overwrite the original Lambda0 Lambda2 format, 16 lambda windows
cat tmp2.txt >> md_forward_1.namd
#To uncomment lines 139 through 141 to turn off the one by one simulation:
sed -i '139,141 s/^/#/' md_forward_1.namd #double check the line numbers.
head -n 123 md_forward_1.namd > outputA
tail -n +124 md_forward_1.namd > outputB
echo "source ../fep.tcl" >> outputA
cat outputB >> outputA
mv outputA md_forward_1.namd
#################### To substitute the alchFile ##############
head -n 13 md_forward_1.namd > output5
cat parameter_patch.txt >> output5
tail -n +14 md_forward_1.namd > output6
sed -i 's/ionized.fep/ionized_solvent.fep/' output6 # correct the B column with -1
sed -i '/^alchDecouple/s/off/yes/' output6 # turn on the "alchDecouple"
cat output6 >> output5
mv output5 md_forward_modi.namd
########Running the job#################################
qsub -I -l select=1:ncpus=32:mem=40gb,walltime=10:00:00 -M your_email@.. -m aeb
cd $PBS_O_WORKDIR
module load intel/18.0.1.163 openmpi/3.1.2-intel namd/2.13-mpi
export Honey_NAMD=/apps/namd/2.13-mpi/arch/Linux-x86_64-icc # this need to be modified.
###################################################################
mpirun --oversubscribe -np 4 $Fuck_NAMD/namd2 +ppn 7 nvt_equil_modi.namd > nvt_equil_modi.out
#NPT###############################################################
mpirun --oversubscribe -np 4 $Fuck_NAMD/namd2 +ppn 7 npt_equil_modi.namd > npt_equil_modi.out
# Production#######################################################
mpirun --oversubscribe -np 4 $Fuck_NAMD/namd2 +ppn 7 md_forward_modi.namd > md_forward_modi.out