[gmx-users] protein structure prediction

[Per Larsson]

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)

Cheers
/Per

>
>
> Mark
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