[AMBER-Developers] issues with born radii

From: Adrian Roitberg <roitberg.ufl.edu>
Date: Thu, 31 Oct 2013 16:20:01 -0400

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