From: Joyce Tan (
Date: Fri Feb 11 2011 - 09:56:39 CST


I've used g_confrms from gromacs to compare two structures with the
following command line -

   g_confrms -f1 1OMB.pdb -f2 md.gro -o fit.pdb

fit.pdb is the output file which would show the 2 structures superimposed on
each other. But when I visualised it with vmd. I can only see one structure.

Any idea what's going on? I hereby attached part of the generated fit.pdb.

All suggestions are welcomed.


  • chemical/x-pdb attachment: fit.pdb