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

Neena Susan Eappen neena.susaneappen at mail.utoronto.ca
Tue Apr 16 21:21:46 CEST 2019

I am using OPLS-AA force field and there are no parameters for protonated carbonyl for alanine residue. How do I go about this?

Thank you,

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,

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