[gmx-users] pdb2gmx with input topology

Ehud Schreiber schreib at compugen.co.il
Thu Apr 28 14:05:52 CEST 2011

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. 





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