Hi,
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)?
Is the correct approach?
Is there any paper on that? I did not found any, but I am not an expert in the matter.
Please note there is no protein involved here.... only two ligands.
Thanks a lot in advance,
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
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Received on Thu Apr 24 2014 - 04:00:03 PDT
