[gmx-users] topology for free energy by perturbation

[Alessandra Villa]

Hi Mikko,

On Mon, 26 Aug 2002, Mikko Huhtala wrote:

> 
> I'm not at all familiar with free energy perturbation
> calculations. I'd like to calculate the free energy difference between
> two small-molecule ligand complexes of a protein. The difference
> between the ligands is a replacement of one -OH group with
> -NH+(CH3)2. Is this too big a difference for perturbation? If not, how
> should the topology be constructed? Can dummy atoms be added to the
> -OH group and then be perturbed into -CH3s?


yes, only if the torsion multiplicity of -*-O- is the same of the torsion 
-*-N- . (see the manual)
If not , I suggest you to mutate  -O-H in dummy and  grow -NH+(CH3)2
group from dummy to real atom. 

best regards 
Alessandra

> 
> Mikko
> 
> 
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