Hi Mark, I tried but with this error:
Fatal error: Number of atoms in pdb frame 0 is 331 instead of 491 Joyce ________________________________ From: Mark Abraham <mark.abra...@anu.edu.au> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Sent: Saturday, February 12, 2011 0:01:39 Subject: Re: [gmx-users] doubts on g_confrms output On 12/02/2011 2:55 AM, Kwee Hong wrote: Hi Tsjerk, > >Thanks for the help. I got it. >But do you have any idea how to solve this in vmd? > Use trjconv -sep on the .pdb file to split it. Mark >Regards, >Joyce > > > > ________________________________ From: Tsjerk Wassenaar <tsje...@gmail.com> >To: Discussion list for GROMACS users <gmx-users@gromacs.org> >Sent: Saturday, January 22, 2011 15:53:22 >Subject: Re: [gmx-users] doubts on g_confrms output > > >Hi Joyce, >In pymol use 'set all_states' >Cheers, >Tsjerk >On Jan 22, 2011 8:30 AM, "Kwee Hong" <jestan1...@yahoo.com> > >wrote: >> >> >>Hi, >> >> >>I was trying to do some analysis following John's >>"GROMACS tutorial for solvation study of spider >>toxin peptide". >>I'm using GROMACS-4.5.3 and my command line for >>g_confrms is >> >> >>g_confrms -f1 1OMB.pdb -f2 md.gro -o fit_wet.pdb >> >> >>The program calculated the RMSD sucessfully and >>fit_wet.pdb was generated. Yet, when i tried to >>visualise fit_wet.pdb using VMD, the structure is >>obviously in a mess. And when I tried it out with >>pymol, I can only visualised one model. Model 2 >>did >>not appear. I wonder would it be the pdb format >>generated by g_confrms is not the standard pdb >>format and had caused VMD and final failed to >>read >>them? >> >> >>Herein, I attached part of the pdb file generated >>by >>fit_wet.pdb. Any insight is welcomed. >> >> >>Thanks, >>Joyce >> >> >>-- >>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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