Re: [gmx-users] conversion of desmond trajectory files into gromacs
Really? This is really great! Is there any need to specify the location of the vmd libraries? If a tpr file is needed for the analysis (eg: trjconv -pbc mol) is this somehow still possible? 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 x.peri...@rug.nl 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 x.peri...@rug.nl 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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. 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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] conversion of desmond trajectory files into gromacs
On Sat, Apr 17, 2010 at 7:54 AM, XAvier Periole x.peri...@rug.nl 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 x.peri...@rug.nl 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 x.peri...@rug.nl 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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. 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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. 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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] conversion of desmond trajectory files into gromacs
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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] conversion of desmond trajectory files into gromacs
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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] conversion of desmond trajectory files into gromacs
Thanks Xavier, Could you make it more eloborate... Ram On Fri, Apr 16, 2010 at 4:38 PM, XAvier Periole x.peri...@rug.nl 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 gmx-us...@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing list gmx-us...@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] conversion of desmond trajectory files into gromacs
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 x.peri...@rug.nl 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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] conversion of desmond trajectory files into gromacs
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 x.peri...@rug.nl 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 x.peri...@rug.nl 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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. 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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
