<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 Mark,<br><br>I tried but with this error:<br><br>Fatal error:<br>Number of atoms in pdb frame 0 is 331 instead of 491<br><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> Mark Abraham <Mark.Abraham@anu.edu.au><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, February 12, 2011 0:01:39<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] doubts on g_confrms output<br></font><br>
On 12/02/2011 2:55 AM, Kwee Hong wrote:
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<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>
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<br>
Use trjconv -sep on the .pdb file to split it.<br>
<br>
Mark<br>
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Regards,<br>
Joyce<br>
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<div style="font-family: arial,helvetica,sans-serif; font-size: 10pt;"><br>
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<hr size="1"><b><span style="font-weight: bold;">From:</span></b>
Tsjerk Wassenaar <a rel="nofollow" class="moz-txt-link-rfc2396E" ymailto="mailto:tsjerkw@gmail.com" target="_blank" href="mailto:tsjerkw@gmail.com"><tsjerkw@gmail.com></a><br>
<b><span style="font-weight: bold;">To:</span></b>
Discussion list for GROMACS users
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<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>
<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>
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<div>Hi,</div>
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<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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</div>
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<br>
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