Right, but I can just warn anyone.
Trying to use TI on a docked structure is insanity...
The docked structure is an approximation in its best case (more likely
its simply crap). Applying a free energy calculation towards such a
structure will give you everything...but sure not the the correct free
energy of binding....except you are very lucky....IF you are that lucky,
play lottery instead and enjoy life ;)
In fact it's (citating Mark) another expensive random number generator...
Regards
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.de
WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
Mark Abraham wrote:
mahbubeh zarrabi wrote:
Dear all
I have 3 complexes of docking.(one receptor with 3
different ligands).I studied MD of 3 complexes in 15
ns by gromacs.how can i compare binding energy and
affinity of 3 ligands with receptor.(how can i
analysis gromacs result)
Shouldn't you have asked this question before designing your
simulations? :-) You can't measure binding affinity without taking a
difference between "before" and "after", which you don't seem to have.
You probably need to look at literature on thermodynamic integration, or
some such.
Mark
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