[gmx-users] How to correct incomplete pdb file
Nathan C. Rockwell
ncrockwell at ucdavis.edu
Thu Nov 17 18:12:28 CET 2005
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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