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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