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: [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"
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