[gmx-users] forcing structure

[Kay Gottschalk]

You can use Modeller for that, I guess.
K.

On Aug 2, 2005, at 4:09 PM, Osmany Guirola Cruz wrote:

> Thanks Magnus, but i need more than a 3d alignament ... there are
> diferrences in the 3d structure of this PDBs.. and i want to force the
> second to fit the first one , forcing the structure in a way that  
> CA of
> the second fit "exactly" in the same positions of the first..sorry  
> if in
> the first mail i don't explain correctly :-)
>
> Osmany
>
>
> On Tue, 2005-08-02 at 15:53 +0200, Magnus Andersson wrote:
>
>>> Hi people,
>>>
>>>   This is may problem :-)
>>> I have 2 PDBs of the same molecule(diferent 3d structure) but the  
>>> first
>>> one only have the CA of the molecule ... then i want to force my  
>>> second
>>> structure(whole protein) to fit the first(CA only) how can i do  
>>> this?
>>>
>>
>> Use g_confrms, use both .pdb files as input and specify which  
>> residues or
>> CA should be aligned in two  .ndx files.
>>
>> Good luck / Magnus
>>
>>
>>> can i use MD?
>>>
>>> Thanks
>>>
>>> Osmany.
>>>
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>>
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Dr. Kay-Eberhard Gottschalk
Department of Applied Physics
Ludwig-Maximilians University
Amalienstr. 54
80799 Munich, Germany

Phone: +49-89-2180 3436