Dear David,
Thanks a lot, no they are not known to form dimers, they form crystals of course but I thought I could learn something about their different interactions or similar using amber. And you are right about they getting apart during the simulation.
They form crystals of course, but I wanted to be able to say something about their "differences" or similarities in forming the crystals or at least about their interactions in solution, as a way to propose experiments or improve the way they are given to the patients (currently two different crystals).
One of their main problems of course is solubility, so I am really firing in the dark for the moment.....
Any suggestion would be great.
Thasnks a lot,
Fabian
On Apr 24, 2014, at 3:07 PM, David A Case <case.biomaps.rutgers.edu> wrote:
> On Thu, Apr 24, 2014, Fabian Glaser wrote:
>>
>> I am interested to calculate the free energy of interaction on many
>> frames of MD for two drug like molecules, I plan the following:
>>
>> 1) Prepare the molecules with antechamber
>> 2) Run MD in vacuum or water
>> 3) Calculate MM-PBSA as you did for a protein-ligand on
>> http://ambermd.org/tutorials/advanced/tutorial3/
>
>>
>> Is that a good idea for two copies of drug molecules (e.g. RITONAVIR)?
>
> In principle, it doesn't matter what the "ligand" and "receptor" are: they
> could both be drug molecules. But is seems likely that the two drug molecules
> may move apart from each other during the MD simulation, which will lead
> to a very small free energy of interaction. But perhaps the molecule is
> known to dimerize(?)
>
> ....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________
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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Apr 24 2014 - 06:00:02 PDT
