AMBER Archive (2009)

Subject: Re: [AMBER] charge consideration

From: case (case_at_biomaps.rutgers.edu)
Date: Sat Sep 12 2009 - 08:59:56 CDT

On Fri, Sep 11, 2009, Jio M wrote:
>
> While docking some charges were assigned .

I'm lost here: what program was used to do the docking? What sorts of charges
were assigned?

> coming
> to my real query, while docking the interaction is made according to
> the charges so assigned to the atoms i.e. the coordinates should change
> if we change the charges.

What are you planning to do after you assign Amber and gaff charges to the
protein and the ligand? You would usually then use this to carry out
minimization or dynamics, and of course the coordinates will then change.
If you do docking in some other program, and then later use Amber, this is the
sort of thing you would expect.

But I probably don't understand your question....

...dac

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