[MMTK] MMTK questions

Nathalie Reuter Nathalie.Reuter at bccs.uib.no
Fri Jul 29 19:09:43 CEST 2005


hi Matias,

>
>I use Amber94, because i need to consider all the
>intramolecular interactions detail.
>
Then, in theory you have to minimize every time you make a change to 
your structure. You need to obtain a minimum on the potential energy 
surface (in order to ensure that the harmonic approximation is valid).

Nathalie


>
>--- Nathalie Reuter <Nathalie.Reuter at bccs.uib.no>
>wrote:
>
>  
>
>>Hi Matias,
>>
>>what force field do you use to perform the normal
>>modes calculation?
>>
>>Regards,
>>Nathalie
>>
>>
>>Matias Saavedra wrote:
>>
>>    
>>
>>>Hi, two simple questions:
>>>
>>>1) If i minimize a protein system, i perform a
>>>      
>>>
>>Normal
>>    
>>
>>>Modes analysis, and the i make a single mutation in
>>>the already minimized system, to perform a new
>>>      
>>>
>>Normal
>>    
>>
>>>Modes analysis... the results of the second
>>>      
>>>
>>analysis,
>>    
>>
>>>in terms of deformations energies or amplitudes,
>>>      
>>>
>>are
>>    
>>
>>>comparable to the results of the first one? I ask
>>>      
>>>
>>that
>>    
>>
>>>because i know that deformation energies and
>>>amplitudes of movement are system-dependent
>>>(qualitative), and can not be directly compared
>>>between diferent systems (proteins)... but what
>>>      
>>>
>>about
>>    
>>
>>>a system that have been slightly modified by a
>>>      
>>>
>>single
>>    
>>
>>>mutation?
>>>
>>>2) Can i use the minimized protein to make a single
>>>mutation and then perform directly a new Normal
>>>      
>>>
>>Modes
>>    
>>
>>>analysis without the need of a new minimization
>>>      
>>>
>>step?
>>    
>>
>>>(i want to perform several Normal modes analysis in
>>>proteins modified by single mutations, and i want
>>>      
>>>
>>to
>>    
>>
>>>avoid the time consuming minimization at each
>>>analysis).
>>>
>>>thanks.
>>>
>>>
>>>
>>>
>>>		
>>>      
>>>
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>>    
>>
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>>>      
>>>
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>>>
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>>>
>>>      
>>>
>>
>>    
>>
>
>
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