ICFF: a new method to incorporate implicit flexibility into an internal coordinate force field.
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 macromolecules. 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 repulsion function for "1-5" and "1-6" interactions to mimic the flexibility of bonds, connecting these atoms. Also, we suggest a way to use a local part of the Cartesian force field to automatically generate fixed covalent geometries, compatible with the ICFF energy function. Here, we present an implementation of the ICFF algorithm, which employs the MMFF94s Cartesian force field as a "source." Extensive benchmarking of ICFF with a representative set of organic molecules demonstrates that the implicit flexibility model accurately reproduces MMFF94s equilibrium conformational energy differences (RMSD approximately 0.64 kcal) and, most importantly, detailed torsion energy profiles (RMSD approximately 0.37 kcal). This accuracy is characteristic of the method, because all the ICFF parameters (except one scaling factor in the "1-5,1-6" repulsion term) are derived directly from the source Cartesian force field and do not depend on any particular molecular set. In contrast, the rigid geometry model with the MMFF94s energy function yields highly biased estimations in this test with the RMSD exceeding 1.2 kcal for the equilibrium energy comparisons and approximately 3.4 kcal for the torsion energy profiles.
Katritch
Vsevolod
V
Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines, TPC-28, La Jolla, California 92037, USA.
Totrov
Maxim
M
Abagyan
Ruben
R