AMBER Archive (2005)

Subject: Re: AMBER: Can GB and MS work correctly together in mmpbsa?

From: Scott Pendley (scott.pendley_at_gmail.com)
Date: Fri Jul 15 2005 - 12:46:46 CDT


That is because you have not put in the parameters of F for the
molsurf program. It is similiar to doing to the modification you did
earlier. If you run into trouble doing this let me know and I will
show you how I did it.

On 7/15/05, zhli_2000_at_126.com <zhli_2000_at_126.com> wrote:
> Hi,
> Thank you for the explanation. But Because there is an atom F in the
> ligand, when I switch MS=1 to MS=0, mmpbsa cann't work correctly. The error
> message is:
> bad atom type: F
>
> What should I do?
> Thank you!
>
>
> >
> > If you switch MS=1 to MS=0, it should work. Energy decomposition does not
> > work so far with a SAS calculation based on MS, but relies on another
> > method approximating atomic surfaces starting from icosahedra.
> > Best regards
> >
> > Holger
> >
> >>
> >
>
>
>
>
>
>
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