<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:arial, helvetica, sans-serif;font-size:10pt"><div>Hi,</div><div style="font-family:arial, helvetica, sans-serif;font-size:10pt"><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><div style="font-family:arial, helvetica, sans-serif;font-size:10pt;"><div style="font-family:arial, helvetica, sans-serif;font-size:10pt;color:#000000;"><div><br></div><div>I was trying to do some analysis following John's "GROMACS tutorial for solvation study of spider toxin peptide".</div><div>I'm using GROMACS-4.5.3 and my command line for g_confrms is </div><div><br></div><div>g_confrms -f1 1OMB.pdb -f2 md.gro -o fit_wet.pdb</div><div><br></div><div>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?</div><div><br></div><div>Herein, I attached part of the pdb file generated by
fit_wet.pdb. Any insight is welcomed.</div><div><br></div><div>Thanks,</div><div>Joyce</div><div style=""></div>
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