[gmx-users] Re: gmx-users digest, Vol 1 #138 - 13 msgs

[Anton Feenstra]

Shang-Te Danny Hsu wrote:
> 
> I took the charge group parameters from NADP in GROMOS96 afterwards. It
> seems okay. But I am not really sure whether it's a proper way to
> parametrize a novel molecule....

It definitely is not. But it often is the only option, and depending
on exactly what type of molecule you are building, possible errors might 
be acceptable. It also depends a lot on what exactly you want to do
with the resulting molecule, i.e. what type of simulations you are
going to run and what specific questions you want to address.

The proper way would involve computation of numerous known parameters,
i.e. density, heat of vaporization, partitioning properties between
different phases (e.g. water/hexane), and the like, and to optimize
the match between the calculated and known values... This can take
a lot (months, years) of time!

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University 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|
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| (    ) | Dept. of Biophysical Chemistry - University of Groningen  |
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|   __   | Tel +31 50 363 4327 - Fax +31 50 363 4800                 |
|  /  \  | K.A.Feenstra at chem.rug.nl - http://md.chem.rug.nl/~anton   |
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|  \__/  | "My Heart is Just a Muscle In a Cavity" (F. Black)        |
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