[gmx-users] Re: ligand force field parameters

[Anton Feenstra]

m b wrote:
>>3.suppose if such parameters are not available to one such ligands of
>>interest can some suggest me means of generating FF parameters.
> 
> 
> The way I normally go is: 
> * use the OPLSAA force field
> * calculate partial charges as ESPD charges with, e.g., ChelpG
>   in Gaussian (or anything compareable) for the ligand
>   (to be consistent this should also be done for the lipid/protein,
>   however, if these are too big then have to use the built-in OPLS charges)

I'm not sure if I would call that 'consistent'. If you consider that
the charges and the other parameters in the forcefield are interdependent,
IMHO it doesn't make sense to replace one set of charges with another...

>>4. re asking previous question best lipids can be used for GPCR simulation
>>studies.
> 
> 
> dunno ... there should be plenty of papers out there ...

Not necessarily, since there are no GPCR crystal structures (only models
based on rhodopsin till now, as far as I'm aware), and setting up and
equilibrating a proten/membrane system is not at all trivial... ;-{


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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