[gmx-users] Gromacs to APBS

Vladimir Lankevich vladimir.lankevich at gmail.com
Wed Jun 30 18:39:25 CEST 2010

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.

Vladimir Lankevich
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