As a follow up to my last note. Specifically you should modify the
generate_pqr() section of mm_pbsa_calceneent.pm. This is the
modification I added to my code . . .
"Na+" => 1.200 + 1.400,
"Cl-" => 1.700 + 1.400,
"MG" => 1.180 + 1.400,
"F" => 1.470 + 1.400,
);
Have fun with this...
On 7/15/05, Scott Pendley <scott.pendley.gmail.com> wrote:
> 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_2000.126.com <zhli_2000.126.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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>
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Received on Fri Jul 15 2005 - 21:53:01 PDT
