On Sat, Apr 17, 2010 at 7:54 AM, XAvier Periole <[email protected]> wrote:
> > Really? This is really great! > Is there any need to specify the location of the vmd libraries? > By default it tries to find them at /usr/local/lib/vmd/plugins/*/molfile If you have them installed somewhere else you can specify it by setting the VMD_PLUGIN_PATH environment variable. If a tpr file is needed for the analysis (eg: trjconv -pbc mol) is this > somehow still possible? > It would be pretty simple to add, that one can read this molecule information also from pdb or from psf. But I didn't have time to do it. In case you are interested to do that, I can give you help doing it. Until someone implements it, one still needs the tpr file. For cases where it is difficult to generate a top file we have a version of psfgen which generates a top file from a psf. But we don't have solved the license issue so far (NAMD license) and thus can't provide this version yet. Roland > > On Apr 16, 2010, at 10:07 PM, Roland Schulz wrote: > > In case you use the GIT version of the analysis tools you don't need to > convert the trajectories first. > I've added that the analysis tools can read all vmd supported file formats > if GROMACS finds the vmd libraries. > > Roland > > On Fri, Apr 16, 2010 at 11:33 AM, XAvier Periole <[email protected]> wrote: > >> >> Well I guess you want to use gmx analysis tools so you'll have to >> build the gmx topology of your system when necessary! Often >> only a pdb file or a gro file is sufficient. >> >> >> On Apr 16, 2010, at 5:24 PM, ram bio wrote: >> >> Thanks Xavier, >>> >>> Could you make it more eloborate... >>> >>> Ram >>> >>> On Fri, Apr 16, 2010 at 4:38 PM, XAvier Periole <[email protected]> >>> wrote: >>> >>>> >>>> VMD reads Desmond trajectories and writes GMX format ... >>>> Rests the topology to deal with ... >>>> >>>> On Apr 16, 2010, at 4:15 PM, ram bio wrote: >>>> >>>> Dear All, >>>>> >>>>> I have run a dynamics of protein ligand complex in lipid bilayer dppc >>>>> using desmond software and would like to convert the trajectory files >>>>> files into gromacs format, is it possible?? if so, please let me know >>>>> your suggestions. >>>>> >>>>> Thanks, >>>>> >>>>> Ram >>>>> -- gmx-users mailing list [email protected] >>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>>>> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php >>>>> >>>> >>>> -- >>>> gmx-users mailing list [email protected] >>>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>>> Please search the archive at http://www.gromacs.org/search before >>>> posting! >>>> Please don't post (un)subscribe requests to the list. Use thewww >>>> interface >>>> or send it to [email protected]. >>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>>> >>>> -- >>> gmx-users mailing list [email protected] >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php >>> >> >> -- >> gmx-users mailing list [email protected] >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use thewww interface >> or send it to [email protected]. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > > > -- > ORNL/UT Center for Molecular Biophysics cmb.ornl.gov > 865-241-1537, ORNL PO BOX 2008 MS6309 > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > > > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309
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