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...) Anna
-----Messaggio originale----- Da: [email protected] [mailto:[email protected]] Per conto di [email protected] Inviato: giovedì 10 marzo 2011 14.15 A: [email protected] Oggetto: gmx-users Digest, Vol 83, Issue 66 Message: 3 Date: Thu, 10 Mar 2011 08:13:06 -0500 From: "Justin A. Lemkul" <[email protected]> Subject: Re: [gmx-users] disulfide bridge broken during EM To: Discussion list for GROMACS users <[email protected]> Message-ID: <[email protected]> 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: [email protected] <mailto:[email protected]> > 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 ======================================== ------------------------------ -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! End of gmx-users Digest, Vol 83, Issue 66 ***************************************** -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
