[gmx-users] -ignh command removes protonation site of interest

Justin Lemkul jalemkul at vt.edu
Tue Apr 16 21:24:10 CEST 2019

On 4/16/19 3:21 PM, Neena Susan Eappen wrote:
> I am using OPLS-AA force field and there are no parameters for protonated carbonyl for alanine residue. How do I go about this?

What exactly are you trying to protonate? The oxygen in a peptide bond 
is not protonated. The C-terminus can be neutralized by selecting the 
"COOH" terminus type interactively using -ter.


> Thank you,
> Neena
> ________________________________
> From: Neena Susan Eappen
> Sent: Monday, April 15, 2019 10:30 PM
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] -ignh command removes protonation site of interest
> Hello gromacs users,
> I started with a peptide where protonation site was on a carbonyl oxygen. However, using -ignh command in pdb2gmx, I lose that proton from there. Any insights on how to move forward?
> Many thanks,
> Neena


Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
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Virginia Tech Department of Biochemistry
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