[gmx-users] Gromacs to APBS

[Vladimir Lankevich]

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.

Cheers,
Vladimir Lankevich
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