As for 1., you will probably need to post-process your trajectory to
get those interactions depending on what you are trying to achieve.
The MM-PBSA tool and cpptraj are probably good places to look into.
As for 2. and 3., the chosen force field would be applied in the same
fashion as to any other interaction. This will be only non-bonded and
electrostatic interactions assuming that your bits and pieces are not
covalently bound to anything.
Cheers,
Hannes.
On Mon, 12 Jan 2015 00:45:11 -0800
Robin Jain <robinjain.chem.gmail.com> wrote:
> Dear Amber Users,
> I am newcomer in molecular dynamics and i want to know following
> things-
>
> 1. What AMBER tells about solute-solute, solvent-solvent and
> solute-solvent interactions.How did it works.
> 2. What parameters are used for this.
> 3. How force fields applied on this.
>
> Thanking You.
>
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Received on Mon Jan 12 2015 - 02:00:03 PST
