<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 Tsjerk,<br><br>Thanks for the help. I got it.<br>But do you have any idea how to solve this in vmd?<br><br>Regards,<br>Joyce<br></div><div style="font-family: arial,helvetica,sans-serif; font-size: 10pt;"><br><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><font face="Tahoma" size="2"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> Tsjerk Wassenaar <tsjerkw@gmail.com><br><b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org><br><b><span style="font-weight: bold;">Sent:</span></b> Saturday, January 22, 2011 15:53:22<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] doubts on g_confrms output<br></font><br><p>Hi Joyce,</p>
<p>In pymol use 'set all_states'</p>
<p>Cheers,</p>
<p>Tsjerk</p>
<p></p><blockquote type="cite">On Jan 22, 2011 8:30 AM, "Kwee Hong" <<a rel="nofollow" ymailto="mailto:jestan1985@yahoo.com" target="_blank" href="mailto:jestan1985@yahoo.com">jestan1985@yahoo.com</a>> wrote:<br><br><div><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: rgb(0, 0, 0);"><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></div>
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