[gmx-users] pH and protein

tarak karmakar tarak20489 at gmail.com
Thu Jul 12 07:42:18 CEST 2012

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 ?
2) how to get the net charge of the protein at that particular pH ? [
Protein Calculator !! ]

Thanks in advance.

Tarak Karmakar
Molecular Simulation Lab.
Chemistry and Physics of Materials Unit
Jawaharlal Nehru Centre for Advanced Scientific Research
Jakkur P. O.
Bangalore - 560 064
Karnataka, INDIA
Ph. (lab) : +91-80-22082809

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