On Mon, 2014-09-08 at 17:35 +0300, Fabian Glaser wrote:
> Oh I see, I thought to use the center of mass starting from a PDB
> structure....yes they are big molecules
> http://en.wikipedia.org/wiki/Ritonavir
> http://en.wikipedia.org/wiki/Darunavir
>
> Their flexibility is not so large since they have 3-4 aromatic rings,
> so you say I cannot use the RDF approach without previously
> equilibrating the system seriously?
If they're not so flexible you may still be able run a simulation with a
box of the molecules and use the RDF to get some idea of their
interactions.
>
> Well, my original idea was to gain some insight at all about their
> interaction, couldn't I first run a single molecule and then freeze
> the best 5 conformations to calculate RDF?
I was talking about inter-molecular RDFs. That obviously won't work
with only a single molecule. In any case, it was just an idea (that may
amount to nothing) to help get you started.
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Sep 08 2014 - 08:00:03 PDT
