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<DIV><FONT face="MS UI Gothic" size=2>Thank you, Erik,</FONT></DIV>
<DIV><FONT face="MS UI Gothic" size=2></FONT> </DIV>
<DIV><FONT face="MS UI Gothic" size=2>I tried Delarue Group's Web Service to
correct 1IAO.pdb.</FONT></DIV>
<DIV><FONT face="MS UI Gothic" size=2>However, 1IAO consists of two chains,
alpha and beta. Moreover, beta chain is a fusion of original beta chain and a
peptide via linker. Due to this construction I think, pdb2gmx did not work
well. The file corrected by SwissPDB Viewer is working well.</FONT></DIV>
<DIV><FONT face="MS UI Gothic" size=2></FONT> </DIV>
<DIV><FONT face="MS UI Gothic" size=2>Thanks,</FONT></DIV>
<DIV><FONT face="MS UI Gothic" size=2></FONT> </DIV>
<DIV><FONT face="MS UI Gothic" size=2>Hiromichi </FONT></DIV>
<BLOCKQUOTE
style="PADDING-RIGHT: 0px; PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #000000 2px solid; MARGIN-RIGHT: 0px">
<DIV style="FONT: 10pt MS UI Gothic">----- Original Message ----- </DIV>
<DIV
style="BACKGROUND: #e4e4e4; FONT: 10pt MS UI Gothic; font-color: black"><B>From:</B>
<A title=lindahl@sbc.su.se href="mailto:lindahl@sbc.su.se">Erik Lindahl</A>
</DIV>
<DIV style="FONT: 10pt MS UI Gothic"><B>To:</B> <A title=gmx-users@gromacs.org
href="mailto:gmx-users@gromacs.org">Discussion list for GROMACS users</A>
</DIV>
<DIV style="FONT: 10pt MS UI Gothic"><B>Sent:</B> Friday, November 18, 2005
7:12 AM</DIV>
<DIV style="FONT: 10pt MS UI Gothic"><B>Subject:</B> Re: [gmx-users] How to
correct incomplete pdb file</DIV>
<DIV><BR></DIV>Hi,
<DIV><BR class=khtml-block-placeholder></DIV>
<DIV>Modeller is quite powerful when building general homology models, but
might be a bit of overkill just to fix a sidechain. You can try a simple
frozen approximation and just scan for individual rotamers - we have a very
naive web implementation (screws up chain identifiers right now) at</DIV>
<DIV><BR class=khtml-block-placeholder></DIV>
<DIV><A
href="http://lorentz.immstr.pasteur.fr/pdb/frozen_submission.php">http://lorentz.immstr.pasteur.fr/pdb/frozen_submission.php</A></DIV>
<DIV><BR class=khtml-block-placeholder></DIV>
<DIV>Cheers,</DIV>
<DIV><BR class=khtml-block-placeholder></DIV>
<DIV>Erik</DIV>
<DIV><BR>
<DIV>
<DIV>On Nov 17, 2005, at 6:12 PM, Nathan C. Rockwell wrote:</DIV><BR
class=Apple-interchange-newline>
<BLOCKQUOTE type="cite"><FONT face="Verdana, Helvetica, Arial"><SPAN
style="FONT-SIZE: 12px">You might try Modeller, available from the Sali lab
web site (salilab.org, I think, but easiest to just google it). Other
options have recently been compared in Protein Science
14:1315-27.<BR><BR>nr<BR><BR><BR>On 11/16/05 7:20 PM, "Hiromichi Tsurui"
<<A
href="mailto:tsurui@med.juntendo.ac.jp">tsurui@med.juntendo.ac.jp</A>>
wrote:<BR><BR></SPAN></FONT>
<BLOCKQUOTE type="cite"><FONT face="Verdana, Helvetica, Arial"><SPAN
style="FONT-SIZE: 12px">Thank you, Tsjerk;<BR> <BR>I would like to
try. But I have never used a kind of modeler soft. Does SwissPDB voewer
works as a modeler soft ? Is it possible to save corrected pdb file using
SwissPDB viewer ? If not, what software is available ?<BR> <BR>Many
Thanks.<BR> <BR>Hiromichi <BR></SPAN></FONT>
<BLOCKQUOTE type="cite"><FONT face="Verdana, Helvetica, Arial"><SPAN
style="FONT-SIZE: 12px"><BR>----- Original Message -----
<BR> <BR><B>From:</B> Tsjerk Wassenaar <A
href="mailto:tsjerkw@gmail.com"><mailto:tsjerkw@gmail.com></A>
<BR> <BR><B>To:</B> Discussion list for GROMACS users <A
href="mailto:gmx-users@gromacs.org"><mailto:gmx-users@gromacs.org></A>
<BR> <BR><B>Sent:</B> Thursday, November 17, 2005
6:00 AM<BR> <BR><B>Subject:</B> Re: [gmx-users] How to
correct incomplete pdb file<BR> <BR><BR><BR>Hi
Hiromichi,<BR><BR>You have to add missing side chains using a
modeler. When you load the protein in SwissPDB Viewer, this will
automatically be done. Be sure to also check the protein for
missing residues. This should be indicated in the PDB file. The
option -ignh is of no use at all in this case.
<BR><BR>Tsjerk<BR><BR></SPAN></FONT></BLOCKQUOTE></BLOCKQUOTE><FONT
face="Verdana, Helvetica, Arial"><SPAN
style="FONT-SIZE: 12px"><BR></SPAN></FONT>
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<DIV>-----------------------------------------------------------</DIV>
<DIV>Erik Lindahl <<A
href="mailto:lindahl@sbc.su.se">lindahl@sbc.su.se</A>></DIV>
<DIV>Assistant Professor, Stockholm Bioinformatics Center</DIV>
<DIV>Stockholm University, SE 106 91 Stockholm</DIV>
<DIV>Phone: +46 8 5537 8564 Fax: +46 8 5537 8214</DIV>
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