[gmx-users] protein structure prediction

[José Carlos Calvo Tudela]

Per Larsson escribió:
>
> 23 feb 2009 kl. 12.55 skrev Mark Abraham:
>
>> José Carlos Calvo Tudela wrote:
>>> can I use the GROMACS software to get the energy of a protein 
>>> conformation?
>>
>> Yes, but your question is not well-formed. Only energy differences 
>> can have meaning.
>>
>>> Up to now I am using TINKER library (analyze program). Is there any 
>>> similar software in GROMACS?
>>
>> I don't know.
>
> If I'm not mistaken, the energy you get from analyse.x  program in 
> Tinker is the potential energy for a protein in is current 
> conformation, given a particular force-field.
>
> In that case, you might be able to get the same from Gromacs if you do 
> a simulation with 0 steps, ie without any integration, and then look 
> at the potential energy terms in the log file (or do many steps, and 
> look at the energy before the first step)
Ok, thank you very much. I will try this
>
> Cheers
> /Per
>
>>
>>
>> Mark
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-- 
José Carlos Calvo Tudela
Miembro del Departamento de Arquitectura y Tecnología de Computadores (http://atc.ugr.es)
y del Equipo de Desarrollo Web de la Universidad de Granada
Universidad de Granada (http://www.ugr.es)


Contacto: jccalvo at atc.ugr.es  
          http://atc.ugr.es/~jccalvo
          34 958 240588   
          646 74 25 54