Yes I understand is for a bunch of molecules, I think I'll give it a go.
Thanks!!
Fabian
_______________________________
Fabian Glaser, PhD
Head of the Structural Bioinformatics section
Bioinformatics Knowledge Unit - BKU
The Lorry I. Lokey Interdisciplinary
Center for Life Sciences and Engineering
Technion - Israel Institute of Technology
Haifa 32000, ISRAEL
fglaser.technion.ac.il
Tel: +972 4 8293701
Fax: +972 4 8225153
On Sep 8, 2014, at 5:58 PM, Jason Swails <jason.swails.gmail.com> wrote:
> 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 - 08:30:02 PDT
