Dear Gromacs users,
I wish to convert PDB files to gromacs format while specifying the topology; however, in the pdb2gmx program, a .top file can only be an output, not an input. The need arises as I have an NMR PDB structure (including hydrogens) which I rather violently perturb into multiple PDB structures using some non-gromacs means. When I convert those structures to .gro using pdb2gmx, sometimes the protonation state of Histidine is guessed incorrectly by the program (the hydrogen moves between HD1 and HE2). Does anybody have a suggestion what can I do? I need the process to be automatic and so can't use the interactive -his option. Thanks, Ehud.
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
