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

[Yang Ye]

Once you have tried it, you will get these questions answered.

Yang Ye

Hiromichi Tsurui 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
>
>
>     -- 
>
>     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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-- 
/Regards,/
Yang Ye
/Computational Biology Lab
School of Biological Sciences
Nanyang Technological University
Singapore
Tel: 6316-2884
/