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

[Hiromichi Tsurui]

Thank you, Yang Ye,

Yes, I have just installed SwissPDB Viewer and am using now.

Many thanks,

Hiromichi

----- Original Message ----- 
From: "Yang Ye" <leafyoung81-group at yahoo.com>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Thursday, November 17, 2005 12:50 PM
Subject: Re: [Bulk] Re: [gmx-users] How to correct incomplete pdb file


> 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
> /
>
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