Hi Tsjerk, Thanks for the help. I got it. But do you have any idea how to solve this in vmd?
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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