[gmx-users] doubts on g_confrms output

Kwee Hong jestan1985 at yahoo.com
Sat Jan 22 08:30:03 CET 2011


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.


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