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<TITLE>Re: [gmx-users] How to correct incomplete pdb file</TITLE>
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<FONT FACE="Verdana, Helvetica, Arial"><SPAN STYLE='font-size:12.0px'>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>
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On 11/16/05 7:20 PM, "Hiromichi Tsurui" <tsurui@med.juntendo.ac.jp> wrote:<BR>
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</SPAN></FONT><BLOCKQUOTE><FONT FACE="Verdana, Helvetica, Arial"><SPAN STYLE='font-size:12.0px'>Thank you, Tsjerk;<BR>
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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>
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Many Thanks.<BR>
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Hiromichi <BR>
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----- Original Message ----- <BR>
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<B>From:</B> Tsjerk Wassenaar <a href="mailto:tsjerkw@gmail.com"><mailto:tsjerkw@gmail.com></a> <BR>
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<B>To:</B> Discussion list for GROMACS users <a href="mailto:gmx-users@gromacs.org"><mailto:gmx-users@gromacs.org></a> <BR>
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<B>Sent:</B> Thursday, November 17, 2005 6:00 AM<BR>
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<B>Subject:</B> Re: [gmx-users] How to correct incomplete pdb file<BR>
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Hi Hiromichi,<BR>
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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>
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Tsjerk<BR>
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