[gmx-users] more than one protonation per residue with pdb2gmx

Justin A. Lemkul jalemkul at vt.edu
Wed Jul 11 16:25:43 CEST 2012

On 7/11/12 10:24 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
> Hi everybody,
> I wanted to ask if there is a possibility to tell pdb2gmx which residues I
> want to be protonated or not.
> So that I can for example say HIS at position 29 shell be protonated twice.
> I need this for further electrostatic analysis.

Please read pdb2gmx -h.  There are tons of available options to control 
protonation of any and all titratable residues.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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