[gmx-users] gromacs result

[Maik Goette]

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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