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On 12/02/2011 3:45 AM, Kwee Hong wrote:
<blockquote cite="mid:976041.85673.qm@web31403.mail.mud.yahoo.com"
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<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>
</div>
</div>
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<br>
OK. I don't know why two frames with different numbers of atoms are
written. Maybe g_confrms -one is useful. Or you can chop apart the
PDB by hand in a text editor.<br>
<br>
Mark<br>
<br>
<blockquote cite="mid:976041.85673.qm@web31403.mail.mud.yahoo.com"
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<hr size="1"><b><span style="font-weight: bold;">From:</span></b>
Mark Abraham <a class="moz-txt-link-rfc2396E" href="mailto:Mark.Abraham@anu.edu.au"><Mark.Abraham@anu.edu.au></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, 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>
</div>
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<br>
Use trjconv -sep on the .pdb file to split it.<br>
<br>
Mark<br>
<br>
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<div><br>
Regards,<br>
Joyce<br>
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<hr size="1"><b><span style="font-weight: bold;">From:</span></b>
Tsjerk Wassenaar <a moz-do-not-send="true"
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<b><span style="font-weight: bold;">To:</span></b>
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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 moz-do-not-send="true"
rel="nofollow"
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wrote:<br>
<br>
<div>
<div style="font-family:
arial,helvetica,sans-serif; font-size: 10pt;">
<div>Hi,</div>
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arial,helvetica,sans-serif; font-size:
10pt;">
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york,times,serif; font-size: 12pt;">
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<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>
<br>
</div>
</div>
</div>
<br>
</div>
<br>
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