[gmx-users] Cys protonation state-Zn modeling

Nuri A Temiz temiz+ at pitt.edu
Sat Feb 11 00:09:03 CET 2006


I am trying to simulate a Zinc-finger domain in solution. I have searched the 
mailing list about Zn-ligand interactions and i decided to fix the Zn since i 
am only interested in keeping the fold stable. 

Of course i need to change the protonation states of 2 CYS and 2 HIS residues.
When i use pdb2gmx, the program automatically protonates the Cys S and His 
NE2. I have checked the manual and fixed the His protonation states, but 
could not change the Cys residues. In the manual, the section for  Pdb2gmx 
says that the program can be prompted to change Cys residue protonation state, 
but i did not see the option to do it.

I must also add that i just started to use Gromacs, so i may be missing 

I would appreciate any help.
thank you very much


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