Anna Marabotti wrote:
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...)
I would not consider the parameters in specbond.dat to be definitive proof of a
non-existent disulfide. If the distance between the S atoms is considerably
more than 0.2 nm (with 0.205 nm being "average" for a disulfide), then you may
have some justification. But if the rationale is "Gromacs didn't think there
should be a disulfide, so that's reality," I'd imagine most reviewers would be
extremely skeptical.
-Justin
Anna
-----Messaggio originale-----
Da: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] Per
conto di gmx-users-requ...@gromacs.org
Inviato: giovedì 10 marzo 2011 14.15
A: gmx-users@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" <jalem...@vt.edu>
Subject: Re: [gmx-users] disulfide bridge broken during EM
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <4d78ce62.2010...@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
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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