[gmx-users] disulfide bridge broken during EM

Justin A. Lemkul jalemkul at vt.edu
Thu Mar 10 14:13:06 CET 2011

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 the 
[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 up) 
to make multiple molecules part of the same [moleculetype].  If you have 
individual chain topologies from pdb2gmx, then there was never a bond there.  If 
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 search 
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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