[gmx-users] Re: disulfide bridge broken during EM

Anna Marabotti anna.marabotti at isa.cnr.it
Thu Mar 10 14:33:44 CET 2011

 Dear Justin,
thank you very much. Yes for sure bonds do not "break" during EM (I should
have better said "disappear"), that's why it looked strange to me. In any
case, I will do the check: if this bond will fall outside specifications in
specbond.dat I will conclude that it is only a crystallographic artefact
(and I will be very happy because in that way I can use only the monomer of
the protein to do simulations...)

-----Messaggio originale-----
Da: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] Per
conto di gmx-users-request at gromacs.org
Inviato: giovedì 10 marzo 2011 14.15
A: gmx-users at gromacs.org
Oggetto: gmx-users Digest, Vol 83, Issue 66

Message: 3
Date: Thu, 10 Mar 2011 08:13:06 -0500
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Subject: Re: [gmx-users] disulfide bridge broken during EM
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4D78CE62.2010601 at vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Anna Marabotti wrote:
> Dear all,
> I have a PDB file of a protein that is in dimeric form, with an 
> INTERchain disulphide bridge. However, in their paper the 
> crystallographers are not sure if this is a true dimeric form or a 
> cyrstallographic artefact (PQS server suggests it is a true dimeric 
> form, but with low confidence). I'm preparing this protein to do MD 
> simulations in water, so I used pdb2gmx, editconf, genbox, genion..and 
> all worked properly (no error messages). Then I launched grompp+mdrun to 
> do a mild minimization before MD: all worked properly with no error 
> messages, but when I had a look at the final .gro file, I saw that the 
> disulphide bridge was broken (before this step, it was present). Looking 
> at the trajectory, I found that the bridge broke at the first step of 
> the minimization. However, I did not have any error message, the 
> minimization worked regularly.
> I would like to know if my starting structure is a real dimeric 
> structure, or not, therefore I would like to know if the disulphide 
> bridge broke because it is only an artefact, or not. Do I have to add 
> some special constraints to the topology and/or .mdp file in order to 
> preserve the disulphide bridge in "normal" simulations, or not? I had a 
> look in the gmx-users list, but I only see suggestions to introduce a 
> new disulphide bridge (and the messages seem quite old, probably 
> referred to the Gromacs 3 version, whereas I'm currently using version 
> 4.0.3). In a very old message (2001) there is the statement "pdb2gmx can 
> *not* make inter-molecular bonds" however, in this case, the bond is 
> already present in the crystal and is kept in all phases until the 
> minimization. I tried to use pdb2gmx -ss in order to set interactively 
> the SS bridge selection, but nothing happened: the program does not ask 
> me any prompt. Any suggestions?

Bonds do not break and form during EM or MD, which must obey classical 
mechanics.  If you saw a "bond" there, it was just an effect of the 
visualization software.  The true answer is if there is a bond written in
[bonds] section of your topology.  While true that Gromacs cannot make bonds

between molecules, you can use pdb2gmx -merge (-chainsep in version 4.5 and
to make multiple molecules part of the same [moleculetype].  If you have 
individual chain topologies from pdb2gmx, then there was never a bond there.
the two atoms fall outside the tolerance range specified in specbond.dat, no

bond will have been created.

> Many thanks and best regards
> Anna Marabotti
> PS BTW: often when I'm searching in the gmx-users list I see the 
> suggestions to some links (for example in the message in 
> http://lists.gromacs.org/pipermail/gmx-users/2008-March/032662.html Mark 
> Abraham suggests to explore 
> http://wiki.gromacs.org/index.php/specbond.dat but when I click on the 
> link, I am redirected to the www.gromacs.org <http://www.gromacs.org> 
> website. Even if I copy the link directly in a new browser window, I 
> cannot see the original link. Why?

The website has undergone several major overhauls since 2008.  You can
the current Gromacs website for specbond.dat and retrieve:



> __________________________________________________________________
> Anna Marabotti, Ph.D.
> Laboratory of Bioinformatics and Computational Biology
> Institute of Food Science - CNR
> Via Roma, 64
> 83100 Avellino
> Phone: +39 0825 299651
> Fax: +39 0825 781585
> E-mail: amarabotti at isa.cnr.it <mailto:amarabotti at isa.cnr.it>
> Skype account: annam1972
> Web site: http://bioinformatica.isa.cnr.it/anna/anna.htm
> "When a man with a gun meets a man with a pen, the man with the gun is a 
> dead man"


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080



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