If you want to emulate leap's behavior, if an atom passes through all of the
logical filters for different elements (of varying connectivities), it's
simply assigned a radius of 1.5 (which may be to prevent crashes or corrupt
sections of the topology... I'm not sure).
All the best,
Jason
On Wed, Aug 17, 2011 at 1:44 PM, Mark Williamson <mjw.mjw.name> wrote:
> Patrick von Glehn wrote:
> > Hi all,
>
> Hi Patrick,
>
> > I don't know the purpose of mapping chemical symbols to Z values.
>
> It is used in the gb_radii assignment routines; you will probably not be
> making use of that.
>
> > Is
> > an acceptable solution to simply add an entry for FE in the source
> > code and then recompile AmberTools?
>
> Yes, that is fine. Ultimately, that routine should have support for
> every element in the periodic table, but seeing that there were only a
> finite number of GB radii parameters, I did not populate that function
> completely.
>
> Regards,
>
> Mark
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Aug 18 2011 - 08:00:04 PDT
