[gmx-users] How to correct incomplete pdb file

[Hiromichi Tsurui]

Thank you, Erik,

I tried Delarue Group's Web Service to correct 1IAO.pdb.
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.

Thanks,

Hiromichi
  ----- Original Message ----- 
  From: Erik Lindahl
  To: Discussion list for GROMACS users
  Sent: Friday, November 18, 2005 7:12 AM
  Subject: Re: [gmx-users] How to correct incomplete pdb file


  Hi,


  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


  http://lorentz.immstr.pasteur.fr/pdb/frozen_submission.php


  Cheers,


  Erik


  On Nov 17, 2005, at 6:12 PM, Nathan C. Rockwell wrote:


    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.

    nr


    On 11/16/05 7:20 PM, "Hiromichi Tsurui" <tsurui at med.juntendo.ac.jp> 
wrote:


      Thank you, Tsjerk;

      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 ?

      Many Thanks.

      Hiromichi


        ----- Original Message ----- 

        From:  Tsjerk  Wassenaar <mailto:tsjerkw at gmail.com>

        To: Discussion list for GROMACS users <mailto:gmx-users at gromacs.org>

        Sent: Thursday, November 17, 2005  6:00 AM

        Subject: Re: [gmx-users] How to  correct incomplete pdb file



        Hi Hiromichi,

        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.

        Tsjerk




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  -----------------------------------------------------------
  Erik Lindahl  <lindahl at sbc.su.se>
  Assistant Professor, Stockholm Bioinformatics Center
  Stockholm University, SE 106 91 Stockholm
  Phone: +46 8 5537 8564     Fax: +46 8 5537 8214










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