On 4/16/18 7:07 AM, mhuht...@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
jalem...@vt.edu | (540) 231-3129
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