[gmx-users] How to correct incomplete pdb file

Hiromichi Tsurui tsurui at med.juntendo.ac.jp
Sun Nov 20 04:08:04 CET 2005

Re: [gmx-users] How to correct incomplete pdb fileThank you Nathan;

I know Modeller. However, at present, it is rather heavy for me. SwissPDB 
viewer seems working well now.

Lot of Thanks,


  ----- Original Message ----- 
  From: Nathan C. Rockwell
  To: Discussion list for GROMACS users
  Sent: Friday, November 18, 2005 2:12 AM
  Subject: Re: [gmx-users] How to correct incomplete pdb file

  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.


  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.


      ----- 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.



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