Justin Lemkul jalemkul at vt.edu
Wed Aug 5 13:46:47 CEST 2015

On 8/5/15 7:12 AM, Akash Deep Biswas wrote:
> 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.

This is not the "source code," rather the installation location.  You can make 
your life easy by sourcing GMXRC, which sets up the environment for you.

> 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.

All GROMACS programs are now modules within a single binary called "gmx."  So 
you need "gmx convert-tpr" and "gmx solvate" to replace tpbconv and genbox, 



> 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
> mdout=mdout.mdp
> log=*.log
> $EDITCONF -f $PROTEINP -o $PROTEINB -c -d 1.0 -bt $BOXT
> $GENION -s $IONTPR -o $PROTEINI -p $TOPOL -pname $PMET -np 5 << EOF
> 13
> 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


Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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