[gmx-users] How to correct incomplete pdb file

[Erik Lindahl]

Hi,

Modeller is quite powerful when building general homology models, but  
might be a bit of overkill just to fix a sidechain. You can try a  
simple frozen approximation and just scan for individual rotamers -  
we have a very naive web implementation (screws up chain identifiers  
right now) at

http://lorentz.immstr.pasteur.fr/pdb/frozen_submission.php

Cheers,

Erik

On Nov 17, 2005, at 6:12 PM, Nathan C. Rockwell wrote:

> 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.
>
> nr
>
>
> 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.
>>
>> 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
>>>
>
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-----------------------------------------------------------
Erik Lindahl  <lindahl at sbc.su.se>
Assistant Professor, Stockholm Bioinformatics Center
Stockholm University, SE 106 91 Stockholm
Phone: +46 8 5537 8564     Fax: +46 8 5537 8214




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