[MMTK] Newby: Protein complex formation

Konrad Hinsen hinsen at cnrs-orleans.fr
Wed Aug 20 18:14:39 CEST 2003


> Then, I used translateBy on each protein separately to put them a small
> distance away from each other. Now I was hoping that the energy
> minimizer would find something close to the initial protein complex.
> That doesn't seem to work, the energy changes but the proteins do not
> move towards each other.
>
> So my questions are:
> 1) Is it at all possible what I am trying to do here? Or am I being too
> optimistic here?

I have never tried this myself. Unless the proteins are strongly charged, the 
forces drawing them together are very weak, so this procedure might take very 
long if it works at all. Also check that you didn't use a cutoff which would 
reduce the interactions too much.

I am by no means an expert in protein-protein interactions, but I suspect that 
solvent plays a major role (hydrophobicity, entropic contributions), so your 
experiment may not be very realistic.

> 2) In MMTK, do the proteins see each other, or are only forces internal
> to the proteins included? I am using the Amber force field. If they

Yes, by default all atoms in a universe interact. You can even calculate 
interaction energies for specific subsets, which might help you understand 
your setup. The details are in the manual (Universe.energyEvaluator), just 
define each protein as one subset and then you can even get a detailed 
breakdown into energy terms by calling the energyTerms method.

> 3) Are the proteins treated as if they were in vacuum, or are they
> assumed to be submerged in water?

The Amber force field is designed to work with explicit solvent. If you don't 
add water molecules, then you simulate the proteins in vacuum.

Konrad.
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