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

donna at iflysib.unlp.edu.ar donna at iflysib.unlp.edu.ar
Fri Sep 12 16:44:25 CEST 2014

Dear Agnivo

Regarding your inquiry: there is an online tool to determine the pka  
value of a protein (of its aminoacids) if you have the pdb file of  
your protein
  The program is "Propka " see it at internet ,( See the paper" "Very  
Fast Empirical Prediction and Rationalization of Protein pKa Values"de  
Hui Li,  Andrew D. Robertson and  Jan H. Jensen,  in PROTEINS:  
Structure, Function, and Bioinformatics 61:704 ?721 (2005))

You should look if the pH, which you need,  is > o < that the corresponding
value of pka and then you should determine  the protonation state of the
protein . The pdb2gmx program has the option of being interactive with  
respect to those aminoacids that have negative or positive charge  
depending of its pka
and the PH ( Glu.Asp, lys, Arg and hys).See that hys at physiological  
pH has no charge.
  Best Regards,

Agnivo Gosai <agnivo2007 at gmail.com> ha escrito:

> 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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