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

[Justin Lemkul]

On 4/17/19 4:13 PM, Neena Susan Eappen wrote:
> 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.

If you're referring to the enol tautomer of the peptide bond, you won't 
find any force field in GROMACS that supports such a species. Moreover, 
all the force fields in GROMACS are designed for the condensed phase 
(though people do use them for vacuum simulations), so you may encounter 
unreasonable behavior.

-Justin

> 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

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
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