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:
http://www.gromacs.org/Documentation/File_Formats/specbond.dat
-Justin
__________________________________________________________________
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: amarabo...@isa.cnr.it <mailto:amarabo...@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
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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