[gmx-users] LIE

[Anton Feenstra]

Alan Wilter Sousa da Silva wrote:
> Hi Dear GMX users!
> 
> 	I did some tests trying to evaluate Linear Interactive Energy
> method to obtain estimatives of free bind energy between protein and
> ligand.
[...]

That looks quite thorough!

> 	So:
> 	First, using PME under any circumstance gave EE very different
> (about half) from RF and Cut-off options.  Should I not expect EE at close
> values independently of the electrostatic treatment?

There is one problem with PME, that it doesn't readily give you the
contributions from separate parts of your system (i.e. ligand and rest).
There was some discussion about this a while back on the list, and a
possible workaround solution was proposed, involving IIRC a re-run
with and without charges on the ligand. Did you use that method?

> 	Second, I would like to know if someone else has, or knows, some
> published references on works using GMX and LIE to indicate me.  I must
> say that I have some references using LIE (from Aquvist, Kollman etc.) but
> none with GMX.

I know it has been used in Amber in our group, with quite some success,
and we're now planning on doing new calculations in Gromacs. No real
results yet, so nothing published either. The Amber work will be
submitted next week, most probably to J.Med.Chem.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
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