----- Original Message ----- From: Vladimir Lankevich <vladimir.lankev...@gmail.com> Date: Thursday, July 1, 2010 2:39 Subject: [gmx-users] Gromacs to APBS To: gmx-users@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? Probably >Also, will this file contain water molecules inputed by gromacs? Yes. >Will this contradict with apbs solvent? Thank you very much. Probably. You can strip these with trjconv -f in.pdb -o out.pdb Mark
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