[gmx-users] help and a tutorial

[Erik Lindahl]

Hi,

You can try a web server we created a while ago at

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

Cheers,

Erik

On Oct 16, 2005, at 12:28 PM, Sebastien Gerega wrote:

> Are there any other programs to do this kind of thing? I have tried  
> using Swiss-PDBViewer and am really having difficulties with it.  
> Doesn't seem to run well on my system and when I try and save my  
> changes as a PDB file it seems to happen ok but then when I go and  
> look for the file it was not created...
>
> Tsjerk Wassenaar wrote:
>
>
>>
>> Hi Sebastien,
>>
>> You shouldn't have used the -missing option. This leaves the atom  
>> out, leaving you with a broken leucine. Apparently the pdb file  
>> has missing atoms. Before setting up a simulation from a pdb file,  
>> first look for missing atoms and residues and fix these if present  
>> (or actually, if not present ;)). The SwissPDB Viewer will  
>> conveniently add missing atoms upon loading a pdb file. Missing  
>> residues will require a bit more effort.
>>
>> The CA-CA2+ warning is ok, if these should be CA2+ that is. The  
>> occupancy unequal to one warning notifies you that some residues  
>> are present in different configurations. This is also not a  
>> problem. In terms of MD it may be good to take both configurations  
>> as starting points.
>>
>> Good luck!
>>
>> Tsjerk
>>
>> --------------------------------------------------------------------- 
>> ---
>>
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>
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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