[gmx-users] disulfide bridge broken during EM

Anna Marabotti anna.marabotti at isa.cnr.it
Thu Mar 10 14:07:29 CET 2011

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?
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
website. Even if I copy the link directly in a new browser window, I cannot
see the original link. Why?
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
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"
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