[gmx-users] Using GROMACS to find the net charge on a Protein

[Justin Lemkul]

On 9/9/14 3:51 PM, Agnivo Gosai wrote:
> Dear Users
>
> I am trying to find the net charge at the physiological pH value for a
> protein molecule (Thrombin) in my case and am wondering if it is possible
> to use GROMACS for doing it.
>
> I am very new to GROMACS and at present I have been going through the
> tutorials by Dr. Lemkul. I have seen that the topology file generated by
> "pdb2gmx" contains the total electron charge value for a molecule.
>
> I was wondering if this can be used to get the charge value for Thrombin at
> physiological pH.
>

Gromacs will assume canonical protonation states at pH 7 for all residues 
(unless you reassign them manually, in which case there's really no point in 
running pdb2gmx because you know the answer).  Whether or not this assumption is 
valid depends on the actual pKa values of the constituent amino acids.  There 
are much more rigorous ways to calculate the net charge of a protein; I'd 
suggest you look at other servers and methods.  There is a huge community of 
people who do pKa predictions.

-Justin

-- 
==================================================

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================