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ICFF: A New Method to Incorporate Implicit Flexibility into an Internal Coordinate Force Field
 

Summary: ICFF: A New Method to Incorporate Implicit Flexibility
into an Internal Coordinate Force Field
VSEVOLOD KATRITCH,1,* MAXIM TOTROV,2
RUBEN ABAGYAN1,2
1
Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines,
TPC-28, La Jolla, California 92037
2
Molsoft, 3366 Torrey Pines Court, La Jolla, California 92037
Received 10 October 2001; Accepted 12 February 2002
Abstract: We introduce a new method to accurately "project" a Cartesian force field onto an internal coordinate
molecular model with fixed-bond geometry. The algorithm automatically generates the Internal Coordinate Force Field
(ICFF), which is a close approximation of the "source" Cartesian force field. The ICFF method reduces the number of
free variables in a model by at least 10-fold and facilitates the fast convergence of geometry optimizations, an advantage
that is critical for many applications such as the docking of flexible ligands or conformational modeling of macromol-
ecules. Although covalent geometry is fixed in an ICFF model, implicit flexibility is incorporated into the force field
parameters in the following two ways. First, we formulate an empirical torsion energy term in ICFF as a sixfold Fourier
series and develop a procedure to calculate the Fourier coefficients from the conformational energy profiles of the fully
flexible Cartesian model. The ICFF torsion parameters thus represent not only torsion component of the source force
field, but also bond bending, bond stretching, and "1-4" van der Waals interactions. Second, we use a soft polynomial

  

Source: Abagyan, Ruben - School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego

 

Collections: Biology and Medicine