The polarizabilities come after the masses in the first section. Check the
file format again, I think it says it there...
The 2 LJ terms come at the last section (NONB), which look similar (and may
lead to confusion).
HTH,
Jason
On Wed, May 4, 2011 at 10:01 PM, r smith <rsl04f.gmail.com> wrote:
> Thanks for the reply, but the problem with frcmod is there doesn't seem to
> be a place for a polarizabilities in that format. With that in mind, I was
> thinking I would need to modify the Amoeba files more fundamentally.
>
> On Wed, May 4, 2011 at 2:26 PM, Ben Roberts <ben.roberts.geek.nz> wrote:
>
> > Hi Rob,
> >
> > On 4/5/2011, at 9:04 a.m., r smith wrote:
> >
> > > Since it appears Amoeba may not recognize the atom types I'm using,
> what
> > > files would need to be modified to add parameters to Amoeba?
> >
> > I think what you would need to do is write an FRCMOD file that supplies
> the
> > missing parameters. For details, see:
> >
> > http://ambermd.org/formats.html#frcmod
> >
> > Can others clarify whether an FRCMOD file works for AMOEBA?
> >
> > Ben
> >
> > --
> > For greater security, I support S/MIME encryption.
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed May 04 2011 - 19:30:02 PDT
