[gmx-users] How to correct incomplete pdb file

Hiromichi Tsurui tsurui at med.juntendo.ac.jp
Thu Nov 17 04:20:56 CET 2005

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
  To: Discussion list for GROMACS users
  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 A. Wassenaar, M.Sc.
  Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
  Dept. of Biophysical Chemistry
  University of Groningen
  Nijenborgh 4
  9747AG Groningen, The Netherlands
  +31 50 363 4336


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