vmd protein.trr protein.gro then go to the representation and then write 'all not water' with cartoon representation, u will get the protein only.
Cheers, Tarak On Thu, Nov 22, 2012 at 12:58 PM, rama david <[email protected]> wrote: > Dear, > -o MT.PnoH.xtc instad of xtc extenstion use pdb you will get pdb file. > And then load it in vmd or pymol u can see it > > On Wed, Nov 21, 2012 at 10:24 PM, Rausch, Felix <[email protected]>wrote: > >> Hi. >> >> Try to load in a .gro file of your system first. After that, use the "load >> data into molecule" option to load in the .xtc. >> >> -----Ursprüngliche Nachricht----- >> Von: [email protected] [mailto:[email protected]] >> Im Auftrag von shch406 >> Gesendet: Mittwoch, 21. November 2012 17:47 >> An: [email protected] >> Betreff: [gmx-users] Vizualization with VMD: no image appears >> >> Dear Gromacs users >> >> To visualize my trajectory with VMD I applied trjconv to .xtc trajectory >> file to eliminate water molecules and velocities remaining protein >> coordinates only. >> However, when I load this reduced file to VMD no image on screen appears, >> nevertheless VMD have identified the file as a "Gromacs compress trajectory >> file". >> What may be the cause of this? >> >> The corresponding command is as follows: >> >> trjconv -f MT.xtc -o MT.PnoH.xtc skip 1 -n defau.ndx -pbc nojump -novel >> >> where MT.xtc contains ~10 frames, defau.ndx is default groups index file. >> Group 2 (Protein-H) was chosen handling dialog. >> >> Merci pour votre collaboration, >> Igor Shchechkin >> >> >> >> >> -- >> View this message in context: >> http://gromacs.5086.n6.nabble.com/Vizualization-with-VMD-no-image-appears-tp5003167.html >> Sent from the GROMACS Users Forum mailing list archive at Nabble.com. >> -- >> 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 >> -- >> 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 >> > -- > 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 -- 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
