On Apr 13, 2010, at 21:23, Alberto Sergio Garay
<[email protected]> wrote:
Dear all
I am preparing the topology for my enzyme molecule using pdb2gmx
tool. But first of all, I run a PROPKA program in order to assign
the correct protonation state for my molecule. As a result of this
calculation I obtained a pair of cysteines which should be
deprotonated at pH 7 (fisiological pH), and others which should be
protonated (the most of them).
I have two questions: 1) Is it a correct aproximation to accept the
protonation state obtained by these kind of methods to assign the
charges of my enzyme's residues?
Depends a lot in how the method is doing it. I never heard of that
one, which does not mean it is bad :))
However diprotonated cysteine at pH 7 is a bit weard! Could it be you
have a di-sulfide bridge?
2) How can I manage to select which cysteines are deprotonated and
which are not, using pdb2gmx tool?
You can get them bridged but not deprotonated. Option -cys IIRC.
Any help will appreciated.
--
Dr. Sergio Garay
Facultad de Bioquimica y Cs. Biológicas
Universidad Nacional del Litoral
Santa Fe - Argentina
C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA
Argentina
Ph. +54 (342) 4575-213
Fax. +54 (342) 4575-221
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