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On 12/02/2011 2:55 AM, Kwee Hong wrote:
<blockquote cite="mid:90003.99691.qm@web31404.mail.mud.yahoo.com"
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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>
<br>
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Regards,<br>
Joyce<br>
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<hr size="1"><b><span style="font-weight: bold;">From:</span></b>
Tsjerk Wassenaar <a class="moz-txt-link-rfc2396E" href="mailto:tsjerkw@gmail.com"><tsjerkw@gmail.com></a><br>
<b><span style="font-weight: bold;">To:</span></b>
Discussion list for GROMACS users
<a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a><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>
<blockquote type="cite">On Jan 22, 2011 8:30 AM, "Kwee Hong"
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wrote:<br>
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<div>Hi,</div>
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york,times,serif; font-size: 12pt;">
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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>
<br>
</div>
</div>
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<br>
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<br>
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