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
fit_wet.pdb
Description: Binary data
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