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

[Neena Susan Eappen]

Hi Justin,

I am trying to simulate a peptide in vacuum and it has been shown that carbonyl oxygen is a favorable site of protonation in gas phase, hence I was looking for protonated carbonyl force field parameters.

Thank you,
Neena
________________________________
From: Neena Susan Eappen
Sent: Tuesday, April 16, 2019 7:21 PM
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: Re: [gmx-users] -ignh command removes protonation site of interest

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,
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