[gmx-users] Cys protonation state-Zn modeling

hnam mahnam at ibb.ut.ac.ir
Sat Feb 11 10:30:40 CET 2006

In the name of God
I think you can try pdb2gmx  ......  -cys 
When you do this command  pdb2gmx ask you about protonation of Cys .
Thank you very much in advance
Institute of  Biochemistry  and  Biophysics (IBB)
Tehran University 
P.O.box 1417614411

-----Original Message-----
From: Nuri A Temiz <temiz+ at pitt.edu>
To: gmx-users at gromacs.org
Date: Fri, 10 Feb 2006 18:09:03 -0500
Subject: [gmx-users] Cys protonation state-Zn modeling

> Hi,
> 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
> something.
> I would appreciate any help.
> thank you very much
> alpay

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