[gmx-users] How to correct incomplete pdb file

[Nathan C. Rockwell]

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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