[gmx-users] SOURCE CODE FOR SOLVATE AND CONVERT-TPR

[Akash Deep Biswas]

Dear Sir,

I am using Gromacs-5.0.6 and i wish to run a .sh script for running a
simulation.

When I write the script i have to mention the source code of the programm.
For ex. for using grompp,

I have to mention the path of the source code of grommpp in the .sh
script. I mention the source code as
/home/akash/programs/GMX-5.0.6/bin/grompp and it is running fine.

Now the problem arises when I wish to use newly developed programs like
"solvate" and "convert-tpr" I do not get the source code in
/my/path/GMX-5.0.6/bin instead i get the source code of GENBOX and TPBCONV
which is again not functional in the latest gromacs-5.0.6 package. Please
help me on how can i mention the programs "SOLVATE" and "CONVERT-TPR" in
my .sh script.

The script that i am using for energy minimization i.e EM.sh file is as
follows:

#!/bin/bash

EDITCONF=/home/akash/programs/GMX-5.0.6/bin/editconf
GENBOX=/home/akash/programs/GMX-5.0.6/bin/genbox
GROMPP=/home/akash/programs/GMX-5.0.6/bin/grompp
GENION=/home/akash/programs/GMX-5.0.6/bin/genion

cwd=/home/akash/Simulation/Protein
PROTEINP=/home/akash/Simulation/Protein/protein_processed.gro
PROTEINB=/home/akash/Simulation/Protein/protein_box.gro
PROTEINW=/home/akash/Simulation/Protein/protein_water.gro
PROTEINI=/home/akash/Simulation/Protein/protein_ion.gro
TOPOL=/home/akash/Simulation/Protein/topol.top
IONMDP=/home/akash/Simulation/Protein/ions.mdp
IONTPR=/home/akash/Simulation/Protein/ions.tpr
BOXT=dodecahedron
CST=spc216
PMET=NA
mdout=mdout.mdp
log=*.log

$EDITCONF -f $PROTEINP -o $PROTEINB -c -d 1.0 -bt $BOXT
$GENBOX -cp $PROTEINB -cs $CST -o $PROTEINW -p $TOPOL
$GROMPP -f $IONMDP -c $PROTEINW -p $TOPOL -o $IONTPR
$GENION -s $IONTPR -o $PROTEINI -p $TOPOL -pname $PMET -np 5 << EOF
13
EOF


Akash Deep Biswas
M.Sc in Bioscience & Bioinformatics
Junior Research Fellow
Department of Biosciences and Bioengineering
Indian Institute of Technology Guwahati,
Assam, 7810369
Ph: +918876088695,+919864461811
Alt. Email: biswasakash95 at gmail.com