[gmx-users] Definiting protonation in pdb2gmx input

Justin Lemkul 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.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
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