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,
Chris
Agnivo Gosai <agnivo2...@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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