Re: [AMBER] Lone Pairs in AMBER FF

From: David A Case <>
Date: Sun, 15 Mar 2020 09:03:55 -0400

On Sun, Mar 15, 2020, 杨明俊 wrote:
> No I don't use the existing force fields with EP. I just add EP based
> on GAFF parameters to examine the halogen bond effect in hydration
> free energy calculation. In this way, how can I prepare the input
> files correctly?

Amber only supports certain types of extra points, and this is not
well-documented, as far as I know. You will need to study the
define_frames() routine in extra_pts.F90 (in the sander code) to see
what is possible. It would be helpful to know where the extra points
you are in mind are located: are the "sigma" points, along the C-Br

Pinging Dave Cerutti here, as he may have more up-to-date information.
This general area is one that we are working on, but the new efforts
have not yet been released.


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Received on Sun Mar 15 2020 - 06:30:04 PDT
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