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

[João Henriques]

Quick answer is no.

In fact, that's really not what (standard) molecular dynamics is for. You
need a constant-pH MD method for that. Read this to get a bit more
acquainted with the subject (might be overkill for you, because I doubt
this is what you want/need):

http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation

Either way, if you really don't need a lot of detail and an approximate
protein net charge will do, why not just look at the pKa's of each amino
acid and try to work out what the net charge would be for a given pH? It's
a quite simple exercise to do with pen and paper and you're never going to
be that far off from reality.
If the protein is too large, just script it or search the web for a tool to
do such. I bet there are a few.

P.S. no.1: pdb2gmx knows nothing about pH. It will set the most likely
charge for each amino acid at pH 7. It's as accurate as the pen and paper
method I suggested. This tool's purpose has little or nothing to do with
what you need.

P.S. no.2: Have you done your literary research properly? I never worked
with thrombin but it doesn't sound very exotic. I bet there are some
titration studies of it.

Best regards,
João Henriques

On Tue, Sep 9, 2014 at 9:51 PM, Agnivo Gosai <agnivo2007 at gmail.com> 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.
>
> Thanks & Regards
>
> Agnivo Gosai
> Graduate Student
> Mechanical Engineering
> Iowa State University
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