Hi Justin and Tsjerk, Thank you for your answers, but I found a command that worked for me:)
First, I concatenated the ensemble of my trajectory. & then, I did the following: trjconv -s a.tpr -f traj.xtc -o traj1.xtc -pbc nojump -n b.ndx Cheers, Carla On Thu, Feb 18, 2010 at 12:47 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Carla Jamous wrote: > >> >> Hi Tsjerk, >> sorry I didn't understand this part of your explanation:"Can you make an >> image of the last frame and send a link >> to it?" >> > > Render an image of your system from the end of your trajectory and post it > somewhere online (like photobucket); do not send it as an attachment to your > email. > > -Justin > > But anyhow, please can you send me the version of trjconv that does the >> trick? >> >> Thanks, >> Carla >> >> On Thu, Feb 18, 2010 at 11:42 AM, Tsjerk Wassenaar <tsje...@gmail.com<mailto: >> tsje...@gmail.com>> wrote: >> >> Hi Carla, >> >> > I checked with genconf & now I'm certain that my ATP molecule is >> still with >> > the protein >> >> That's good to know :) >> >> >>> trjconv -s a.tpr -f b.xtc -o c.xtc -center -ur compact -pbc mol >> >>> (centering on "Protein") >> >> So what did come out of this then? It should have given you a compact >> representation of your system with the protein in the center. But if >> the protein's in the center and everything is put as close to that >> center as possible, which is what "compact" does, then the ATP should >> be there too. Can you make an image of the last frame and send a link >> to it? Alternatively, I have a patched version of trjconv that you can >> use to do the trick. I can send it if you want. >> >> Cheers, >> >> Tsjerk >> >> >> -- >> Tsjerk A. Wassenaar, Ph.D. >> >> Computational Chemist >> Medicinal Chemist >> Neuropharmacologist >> -- >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-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 >> <mailto:gmx-users-requ...@gromacs.org>. >> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-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 >
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