[gmx-users] protonation_states

Rita Melo ritamelo at ctn.ist.utl.pt
Thu Dec 31 15:18:57 CET 2015


To calculate the pka values, you can use the PROPKA system.

Have a nice 2016, everyone!!

-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se
[mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of
Justin Lemkul
Sent: quinta-feira, 31 de Dezembro de 2015 14:07
To: gmx-users at gromacs.org; Sana Saeed
Subject: Re: [gmx-users] protonation_states

On 12/31/15 1:15 AM, Sana Saeed wrote:
> hi gmx users
> what should be the protonation states of of amino acids LYS, ARG, ASP, 
> GLU, GLN and HIS at PH 2

I already provided suggestions for this.  You need to calculate pKa values. 
This is not a GROMACS question, so please look up some basic biochemistry
and apply Google as needed.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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