[gmx-users] Definiting protonation in pdb2gmx input
jalemkul at vt.edu
Mon Apr 16 13:55:28 CEST 2018
On 4/16/18 7:07 AM, mhuhtala at abo.fi wrote:
> One of the recurring questions on the list seems to be how to define
> residue protonation states non-interactively in pdb2gmx input. The
> interactive options are a bit of a nightmare to use. Could pdb2gmx be
> modified to optionally read the residue types from the PDB file
> itself? The user would replace e.g. "ASP " with "ASPH" in the PDB
> file, and pdb2gmx would build a protonated aspartate, whether the
> hydrogen atom is there in the PDB file or not. Same for all residue
> types, of course. The upside would be having readable and more easily
> scriptable input instead of trying to script the interactive input. I
> realize that the names of the residue types differ between force
> fields, but even requiring force field specific names would be ok as
> far as I'm concerned (ASPH in Gromos, ASH in Amber, etc.).
I just tested this in GROMACS 2018 and it works fine - if you provide
the protonated residue name, pdb2gmx correctly interprets the
protonation state. Do you have a use case that fails?
Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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