AMBER Archive (2003)

Subject: Re: AMBER: Fluorine in GBSA

From: Alexey Onufriev (onufriev_at_scripps.edu)
Date: Tue Nov 25 2003 - 15:33:43 CST

gbsa = 0 means you are neglecting changes in is the surface energy. So, if
you don't expect large conformational changes that's probably OK.

Even if you do, trying gbsa=0 first is OK, it'll give you a good idea of
what to expect.

                                                                Alexey

On Mon, 24 Nov 2003 aini_at_UMDNJ.EDU wrote:

> Dear Ambers,
>
> I am trying to run a MD simulation on protein-ligand complex using GBSA. One
> thing troubled me is that my ligand has F atom and sander doesn't have surface
> area parameter for this atom. If I use gbsa = 0, the sander will run. My
> question is if this kind of simulation (gbsa = 0) is reasonable using GB. And do
> I need to modify some other parameters to accomadate gbsa = 0.
> Thank you very much!
>
> aini
>
>
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