Hi,
I think there are really two issues here. One is the somewhat
arbitrary way that LEaP assigns GB radii, the other is that there is
(at least I think) no definitive database for all Amber atom types.
A google search for "amber atom type" brings up several results, but
other than the GAFF page there are no results from ambermd.org (at
least on the first page). I think there needs to be a central data
base of Amber atom types (including GAFF, GLYCAM, etc). This way
anyone developing new parameters has one place to check for existing
atom type names (as well as guidelines on how to create type names). I
know there has been talk of doing this in the past, but I'm not sure
if any progress has been made.
As far as assigning GB radii, I agree with Jason that the long term
solution is to assign parameters like these based on chemical
knowledge. I think the easiest way to do this going forward may be to
have an additional atom type parameter that is the unambiguous atom
type based solely on chemical environment; i.e. something like 'sp3
carbon' == 'Amber type CT' == 'GAFF c3' == unambiguous type 0, 'amide
H' == 'Amber type H' == 'GAFF hn' == unambiguous type 1, etc.
-Dan
On Thu, Oct 31, 2013 at 2:20 PM, Adrian Roitberg <roitberg.ufl.edu> wrote:
> Hi All,
>
> I found a peculiar behavior that I need help solving.
>
> 99SBildn has created some new atom types that seems to conflict with
> other names. In particular, ILE has a new C3 type, associated with the
> CG2 carbon atom.
>
> Tleap assign that CG2 as C3, and if one uses GB, it assign a value of
> the Born radii of 2.2, clearly too large.
>
> Same exact setup with ff99SB, assigns a CT type to CG2, and a born radii
> of 1.7
>
>
> The conflict seems to be with C3 atom names being present in some
> version of the UA FFs and also in nucleic acids.
>
> I do not want to start a flame war about how to solve the overall atom
> name issue, but rather to see if someone can come up with a clever
> solution short term (besides editing the prmtop !) and to tell anyone
> that has used ildn with GB to be very careful and check their results...
>
>
> --
> Dr. Adrian E. Roitberg
>
> Colonel Allan R. and Margaret G. Crow Term Professor.
> Quantum Theory Project, Department of Chemistry
> University of Florida
> roitberg.ufl.edu
> 352-392-6972
>
>
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Fri Nov 01 2013 - 10:30:07 PDT
