[gmx-users] Disulfide between protein Cys and GSH

한상화 hansh at kangwon.ac.kr
Wed Jan 17 07:52:39 CET 2007

I am sorry, Mark. I didn't mean to make you feel bad.
But I'll keep what you said in mind.
Thank you.
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 3:45 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Disulfide between protein Cys and GSH

한상화 wrote:
> 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.

Try reading about the -merge option for pdb2gmx.

For the record, I don't appreciate being asked to provide instructions
for a procedure, and then to be told you've apparently done just that
before asking for someone to describe the procedure. You will get a far
better response from a wider range of people, if you document your
procedure and ask for feedback and criticism. Further, the person
providing the free help doesn't get made to feel like they were wasting
their time re-doing your work.

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