Alright.. I actually simulated my protein for 5ns. Then I loaded the trajectory file and .gro file in vmd. Then, I extracted one of the frame and write it into pdb format, When I open it with vmd, one of the atom from a residue is connected to another atom in another residue. Things like this happens as VMD uses a distance-based bond determination heuristic. Therefore, I would need a structure file which specifies the bonds for my structure so that VMD doesn't have to guess.
So how can I generate the structure file I needed? Thanks. Regards, Joyce ________________________________ From: Justin A. Lemkul <jalem...@vt.edu> To: Gromacs Users' List <gmx-users@gromacs.org> Sent: Wednesday, October 20, 2010 2:25:26 Subject: Re: [gmx-users] top2psf.pl is generating some bonds to atoms with index 0. Kwee Hong wrote: > I executed the script at the therminal by typing > perl top2psf.pl -i topol.top -o zz.psf > Here, I attached my input file. > Your topology does not correspond to a MARTINI coarse-grained topology. As such, probably a bunch of the pattern matching is getting incorrect information. You cannot use top2psf.pl with this type of topology. It was created for a very specific purpose and requires that format, nothing else. -Justin > ------------------------------------------------------------------------ > *From:* Justin A. Lemkul <jalem...@vt.edu> > *To:* Discussion list for GROMACS users <gmx-users@gromacs.org> > *Sent:* Wednesday, October 20, 2010 2:14:34 > *Subject:* Re: [gmx-users] top2psf.pl is generating some bonds to atoms with >index 0. > > > > Kwee Hong wrote: > > Hi, > > > > I've got a top2psf.pl script from the web and used it to generate a psf >file. Yet it generated some bonds to atoms with index 0 which should not >occur. It causes VMD cannot load it and had a segmentation fault. > > vmd > Info) Using plugin psf for structure file /home/birg/Desktop/zz.psf > > ERROR) Error reading bond information. > > Segmentation fault > > > > I wonder am I getting the right top2psf.pl. Or is there any place I can > get >the latest stable version of that script? > > > > There is only one version. Zeros are only printed if something goes wrong, >i.e. you have provided the wrong input or something else has failed. > > Based solely on the information you've provided I cannot diagnose what has > gone >wrong. > > -Justin > > > Here, I attached the perl script I used. > > > > Thanks. > > > > Regards, > > Joyce > > > > -- ======================================== > > 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 ><mailto:gmx-users@gromacs.org> > 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 gmx-users-requ...@gromacs.org ><mailto:gmx-users-requ...@gromacs.org>. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- ======================================== 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/Support/Mailing_Lists/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/Support/Mailing_Lists
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