On 5/16/12 7:13 AM, Acoot Brett wrote:
Dear All,
Will you please tell me how GROMACS calculates the total charge of a protein at
pH 6.5? And how do we assign the ionization state of the residues, especially
for HIS at pH 6.5?
Gromacs does not automatically deal with anything aside from pH 7 protonation
states, though for most residues the difference between 6.5 and 7 is irrelevant.
Histidine protonation is assigned based on a hydrogen bonding search. If you
need to adjust protonation states, you need to do so yourself, but at pH 6.5 it
will be very tricky to deal with those histidines.
-Justin
--
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Justin A. Lemkul, Ph.D.
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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