The spheres will play the role of inert (i.e. only vdw interactions)
crowders for the macromolecule of interest. Each sphere should have a
radius of (say) 50 Angs. The spheres are supposed to mimic the effect of
inert crowders like Ficoll.
On Tue, Nov 11, 2014 at 5:17 PM, David A Case <case.biomaps.rutgers.edu>
wrote:
> On Tue, Nov 11, 2014, ATUL KUMAR wrote:
>
> > I want to represent a molecule with a sphere and my system would be a
> > macromolecule + spheres. Spheres have only Van der waals interaction, no
> > charge and it does not make any covalent bond. So, I need to put only
> mass
> > and VDW parameters for the sphere in AMBER. I am trying to find a good
> set
> > of vdw parameters for my sphere. Has anybody done like this? Any pointer
> > would be appreciated.
>
> I don't think anyone could answer this question without knowing what the
> spheres are supposed to represent.
>
> ....dac
>
>
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Received on Tue Nov 11 2014 - 23:00:02 PST
