[gmx-users] Changing the pH
joao.henriques.32353 at gmail.com
Tue May 10 18:45:28 CEST 2011
Perhaps you should try one of the available constant-pH MD methods. Here is
a quick explanation of what they do and who is involved in their development
My opinion regarding this subject may be a little biased since I've worked
with one of the most active researchers in this area, but I would suggest
you to read some papers from Antonio Baptista and/or Miguel Machuqueiro
(from Baptista's 2002 initial "Constant-pH molecular dynamics using
stochastic titration" paper to nowadays).
On Tue, May 10, 2011 at 7:22 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> 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.
>> 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
>> This message was sent using IMP, the Internet Messaging Program.
> 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
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João Henriques, MSc in Biochemistry
Faculty of Science of the University of Lisbon
Department of Chemistry and Biochemistry
C8 Building, Room 8.5.47
Campo Grande, 1749-016 Lisbon, Portugal
E-mail: joao.henriques.32353 at gmail.com / jmhenriques at fc.ul.pt
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