[gmx-users] Gromacs to APBS

Mark Abraham mark.abraham at anu.edu.au
Thu Jul 1 02:27:44 CEST 2010

----- Original Message -----
From: Vladimir Lankevich <vladimir.lankevich at gmail.com>
Date: Thursday, July 1, 2010 2:39
Subject: [gmx-users] Gromacs to APBS
To: gmx-users at gromacs.org

> Dear Gromacs users, >   > I need to determine electric potential on each atom, and I know that APBS has such function. I wanted to first minimize the energies through gromacs and then use the apbs to do the electrostatic calculations. Can you please tell me what file do I need to convert to pqr after running energy minimization? I have read in one of the letters in the archive that editconf can turn .tpr into .pqr through -mead option, but this confused me, because mdrun does not give .tpr files as output. Should I just use -c option to get a .pdb file and the convert it to .pqr? 


>Also, will this file contain water molecules inputed by gromacs? 


>Will this contradict with apbs solvent?  Thank you very much.
Probably. You can strip these with trjconv -f in.pdb -o out.pdb


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