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Hi,<br><br>It is not a pdb2gmx feature, but a global one.<br>pdb2gmx is only affected in the sense that it retains the residue numbers from the input pdb.<br>I assume those will be different for most lipid pdb files (if you use pdb2gmx for those).<br>This renumbering is done by any program that needs to output or select global residue numbers.<br>Currently this is switchable with the env.var. I mentioned.<br>If you put this env.var. in your GMXRC, you can get things how you want them.<br>Adding an option to all programs is not a good idea.<br><br>But I am open for any suggestions on this issue.<br><br>There is something I don't get though.<br>In the problematic output the lipids can not be one single residue, but should be two or more residues.<br><br>Berk<br><br>> Date: Mon, 18 Jan 2010 10:31:19 -0500<br>> From: jalemkul@vt.edu<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] trjconv problem<br>> <br>> <br>> Could renumbering be a switchable feature? For instance, pdb2gmx -[no]renumber, <br>> with "no" being default? Otherwise, could you provide an example of how to <br>> properly use the environment variable you posted, since this would seem to <br>> affect all of us in the membrane protein world quite distinctly (i.e., a <br>> singly-numbered lipid, as reported, kills many of the programs we have written <br>> for lipid analysis).<br>> <br>> -Justin<br>> <br>> Berk Hess wrote:<br>> > Hi,<br>> > <br>> > This is a feature.<br>> > For a long time users have been complaining that pdb2gmx renumbers the <br>> > residues in a protein.<br>> > I have now changed this such that the residue numbers in the pdb are <br>> > retained.<br>> > But for for instance solvent you would not like to have this behavior.<br>> > So I decided to keep numbering single-residue molecules.<br>> > If you also want you lipids to continue numbering, you'll have to set <br>> > the env.var. GMX_MAXRESRENUM<br>> > to the number of residues in a lipid.<br>> > <br>> > Berk<br>> > <br>> > ------------------------------------------------------------------------<br>> > Date: Mon, 18 Jan 2010 13:05:42 -0200<br>> > From: stefhoor@gmail.com<br>> > To: gmx-users@gromacs.org<br>> > Subject: [gmx-users] trjconv problem<br>> > <br>> > I am trying to use trjconv to extract frames from my protein/membrane <br>> > system in order to analyse with gdmat. Before using git's latest gromacs <br>> > version, everything worked just fine. But now, every coordinate file <br>> > trjconv gives me has the DPPC lipid molecules without numbering. It is <br>> > like if my membrane was formed of a single DPPC (huge) residue. So <br>> > instead of generating DPPC residue 1, 2, 3, 4 ....etc, trjconv gives me <br>> > DPPC residue 1 with 5000 atoms.<br>> > Some light on the matter would be great.<br>> > Thanks<br>> > <br>> > <br>> > ------------------------------------------------------------------------<br>> > New Windows 7: Find the right PC for you. Learn more. <br>> > <http://windows.microsoft.com/shop><br>> > <br>> <br>> -- <br>> ========================================<br>> <br>> Justin A. Lemkul<br>> Ph.D. Candidate<br>> ICTAS Doctoral Scholar<br>> MILES-IGERT Trainee<br>> Department of Biochemistry<br>> Virginia Tech<br>> Blacksburg, VA<br>> jalemkul[at]vt.edu | (540) 231-9080<br>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>> <br>> ========================================<br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br> <br /><hr />New Windows 7: Find the right PC for you. <a href='http://windows.microsoft.com/shop' target='_new'>Learn more.</a></body>
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