On 7/12/12 1:42 AM, tarak karmakar wrote:
Dear All,
I am simulating a protein in gromacs with amber force field. The
protein shows maximum biological activity at pH 5.0 and at pH 7.4 it
shows no activity. So whichever biological process I am going to model
should be at the biologically active pH . So can anyone suggest me
1) how to get the protonation state of each and every residues present
in the protein at that particular pH [i.e. at pH 5.00] ? Should I look
into the pKa values of each and every residues from standard table to
or is there any software to find the same ?
pKa values can vary greatly depending on the local environment of the residue.
You should find a method to calculate the pKa values. One possibility:
http://biophysics.cs.vt.edu/
2) how to get the net charge of the protein at that particular pH ? [
Protein Calculator !! ]
The net charge is printed in the topology produced by pdb2gmx.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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