Tanos Celmar Costa Franca wrote:
Dear GROMACS users,
Does someone now how to procede to change the pH of a MD simulation from
the physiologic one (7.4) to 6.5 ?
Classical MD simulations do not currently allow for dynamic proton exchange.
The best you can do at the moment is use pdb2gmx to set the protonation state of
titratable residues. At pH 6.5, histidines will be quite annoying to deal with
properly.
-Justin
Tanos Celmar Costa Franca - D.Sc
Coordenador do Programa de Pos-graduacão em Química
Secão de Engenharia Química - SE/5
Instituto Militar de Engenharia - IME
Rio de Janeiro - RJ
Brasil
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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