[gmx-users] LIE

[David van der Spoel]

On Wed, 2003-03-19 at 14:54, 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.
> 
> 	I tried using Reaction Field, Cut-off and PME, with and without
> ions or neutralising proteins (by protonation or deprotonation of some
> residues).
> 
> 	I did dynamics of 600 ps, 1 ns or more using Gromos96 FF, with box
> at least 1.5 nm bigger than the complex and rc not greater than 1.4 nm, t
> and p-coupling = berendsen.
> 
> 	Evaluating only van der Waals energy (LJE) I got good results in
> agreement for all cases studied.
> 
> 	However Electrostatic Energy (EE) gave me very unexpected results.
> 
> 	Despite the fluctuations in energy that led, in some cases,
> to big RMSDs (implying unacceptable error estimation) I got in general
> that EE for ligand in solvent are more negative than EE for ligand in
> protein, which implies positive values for delta EE (quite weird!)
> 	Even considering the fact that my ligands topology could be wrong
> (I tried with 4 different ligands), I tried one peptide ligand and a
> dimeric protein (to calculate the EE between the two chains).
> 	Even for these two later cases I got strange results for EE.
> Well, there was only one situation where I got negative values for delta
> EE and that happen when I use R. Field (with epsilon=0 and =80) without
> ions and neutralised protein.
> 
> 	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?
With PME you need to do extra simulations to compute the contribution of
the protein-ligand to the long-range Coulomb. This has been described
before on the list.


> 	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.
Nothing published yet I'm afraid...

> 
> 	If someone has interest in obtain more details about what was done
> above, you may e-mail me directly.
> 
> Many thanks in advance for any attention. I'd appreciate very well any
> commentary.
> 
> Cheers,
> 
> -----------------------
> Alan Wilter S. da Silva
> -----------------------
>  Laboratório de Física Biológica
>   Instituto de Biofísica Carlos Chagas Filho
>    Universidade do Brasil/UFRJ
>     Rio de Janeiro, Brasil
> 
> 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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