[gmx-users] Question about setting deprotonated cys in enzyme structure ....

XAvier Periole x.periole at rug.nl
Tue Apr 13 23:16:00 CEST 2010

On Apr 13, 2010, at 21:23, Alberto Sergio Garay  
<sgaray at fbcb.unl.edu.ar> 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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