Also I must to point out that all simulation will be performed in the
bergers lipids interior ( I'm simulating membrane bound receptors with the
hormone-like ligands)
James
2013/4/8 James Starlight <jmsstarlight.gmail.com>
> Dear Amber's users!
>
> I want to perform list of full atomic simulation of protein-ligand
> complexes in Gromacs using Amber99sb force field and ligand parametrized by
> means of antechamber (acpype).
>
> 1- From antechamber tutorials I've found that GAFF is used for such ligand
> parametrization. What cut-offs for electrostatics as well as vdw should I
> use for the modelling of protein-ligand complexes ? (assuming that I've
> used 1.0 cutoffs with such systems without ligands)
>
> 2- How I can assign charges more carefully ? Could you provide me with
> some example of such charges assignment based on different chemical
> compounds?
>
>
> Thanks for help,
>
> James
>
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Received on Mon Apr 08 2013 - 05:00:04 PDT
