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

Alberto Sergio Garay sgaray at fbcb.unl.edu.ar
Tue Apr 13 21:23:12 CEST 2010

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?

2) How can I manage to select which cysteines are deprotonated and  
which are not, using pdb2gmx tool?

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
Ph. +54 (342) 4575-213
Fax. +54 (342) 4575-221

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