[gmx-users] doubts on g_confrms output

[Tsjerk Wassenaar]

Hi Joyce,

In pymol use 'set all_states'

Cheers,

Tsjerk

On Jan 22, 2011 8:30 AM, "Kwee Hong" <jestan1985 at 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



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