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

Agnivo Gosai agnivo2007 at gmail.com
Tue Sep 9 21:51:05 CEST 2014

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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