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
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Received on Thu Oct 31 2013 - 13:30:03 PDT
