[gmx-users] Fwd: Deprotonated Cys

[David van der Spoel]

If the Cys is bound to a heme iron it should work out of the box, but 
only for certain force fields.

from specbond.dat:

CYS     SG      1       CYS     SG      1       0.2     CYS2    CYS2
CYS     SG      1       HEME    FE      2       0.25    CYS2    HEME
CYS     SG      1       HEME    CAB     1       0.18    CYS2    HEME
CYS     SG      1       HEME    CAC     1       0.18    CYS2    HEME

-------- Original Message --------
Subject: 	Deprotonated Cys
Date: 	Thu, 18 Mar 2010 18:46:52 -0400
From: 	Somayesadat Badieyan <badieyan at vt.edu>
To: 	<spoel at xray.bmc.uu.se>



Dear Dr. Spoel,

I would like to modeled my protein using gromacs. My structure has a Cys
that is involved in a S-salt-bridge to a Heme group. I found that
Gromacs does not support any charged Cys. In the gromacs email list I
found that you have the topology for a deprotonated Cys, made from some
quantum calculations. I appreciate, if possible, send that topology file
for deporotonated Cys to me.

Thanks you

Somaye

/.................................................................../

*/Somayesadat Badieyan/*

*/PhD Candidate and Research Assistant /*

*/Biological Syatems Engineering/*

*/201 Seitz Hall, Virginia Tech/*

*/Blacksburg, VA/*

/.................................................................../