[gmx-users] doubts on g_confrms output

Tsjerk Wassenaar tsjerkw at gmail.com
Sat Jan 22 08:53:22 CET 2011

Hi Joyce,

In pymol use 'set all_states'



On Jan 22, 2011 8:30 AM, "Kwee Hong" <jestan1985 at yahoo.com> wrote:


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.


gmx-users mailing list    gmx-users at gromacs.org
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-request at gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110122/0a6e7b4e/attachment.html>

More information about the gromacs.org_gmx-users mailing list