[gmx-users] Disulfide between protein Cys and GSH

한상화 hansh at kangwon.ac.kr
Wed Jan 17 07:23:48 CET 2007

Thank you Mark.
The method you suggest is exactly what I tried.
I prepared a structure of two molecules in which the S...S distance was
made to be 0.206 nm (this value is within the tolerance).
But when I ran pdb2gmx -ignh -ss, it only asked me to form intramolecular
disulfides. It did not ask for intermolecular disulfide.

Sanghwa han

-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of Mark Abraham
Sent: Wednesday, January 17, 2007 3:09 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Disulfide between protein Cys and GSH

한상화 wrote:
> Dear Mark,
> Could you kindly tell me how it can be done?

The general procedure is to get a structure with the relevant S atoms
close enough together, then use pdb2gmx -ss on that structure (possibly
with -ignh too). You may need to copy specbond.dat from the library to
your working directory and edit it to increase tolerance for SS bond or
similar. You may need to do an MD simulation with a harmonic restraint
to position the sulfur atoms close enough for the new structure to be
vaguely realistic.

> Or tell me where in the manual to look up?

Unfortunately it isn't there. Searching the mailing lists from the
gromacs webpage is a good start, though.

> What I am trying to do is either generating a new residue CysS-SG (named
> CYG, for example) or forming a disulfide between CysSH and GSH during
> running Gromacs (I am not sure if there is a command or flag for this
> purpose). 

You'll have to be prepared to get your hands dirty for the former, but
the latter should be painless (not that I've ever done it).

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