[gmx-users] PRODRG - .itp file

[Anton Feenstra]

Luciane Vieira de Mello wrote:
> 
> Dear Anton,
> 
> >
> > You have quite a number of (heavily charged) oxygens in your molecule,
> > which fall outside the exclusions. Also, both the PO4 group and the CO2
> > group carry a net -1 charge. It might be that these forces cause your
> > distortion.
> >
> 
> It seems the charge of the molecule is really the problem, as you pointed
> it out. I performed EM in vacuo, and I got no distortion of the angles.
> But, unfortunately, the ligand is charged when bound to the protein, so
> I should have it charged in the system.
> Have you got any idea of how I could minimize the distortion!? any
> parameters which could be changed in order to achieve a better result?

My guess is you should introduce (additional) exclusions for those
charge interactions that are the (main) cause of the distortions.
However, I am not the expert in designing small molecule topologies
and forcefields. That is why I've also directed this mail back into
the list...


-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
| |----  | De Boelelaan 1083 - 1081 HV Amsterdam - The Netherlands   |
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| ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
|  /  \  |-----------------------------------------------------------|
| (    ) | Dept. of Biophysical Chemistry - University of Groningen  |
|  \__/  | Nijenborgh 4 - 9747 AG Groningen - The Netherlands        |
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