[gmx-users] pH and protein

Justin A. Lemkul jalemkul at vt.edu
Thu Jul 12 12:06:22 CEST 2012

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:


> 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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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