Largescalesimulationsofmacromoleculesinsolutionthatdonot suffer from artifacts arising from force truncations are becoming feasible. New force evaluation algorithms such as the Fast Multipole Method (FMM) and multiple time scale integration methods such as the reversible Reference System Propogator Algorithm (r-RESPS) have been combined and used to perform fast and stable simulations of large macromolecular systems. A consistent treatment of the long-range forces in simulations with periodic boundary conditions requires the use of a periodic form of the Coulomb potential. In a previous publication we have discussed the origin and relevance from computer simulations of a strong finite-size effect which appears when using the Ewald summation formula and affects the electrostatic interaction energies. It can be understood as arising from a volume-dependent shift of the potential in a finite, periodic box relative to the infinite volume limit. This shift is due to the fact that the """"""""zero of energy"""""""" for a periodic system cannot be defined by letting the interacting particles be separated by an infinite distance; the correct definition corresponds to setting its k = 0 Fourier mode to zero. Other groups have discussed related but different finite size effects in the context of the free energy of charging an ion. One of the goals of our studies is to determine to what extent do these finite-size effects affect the pKa calculations on a system as complex as a protein.

Agency
National Institute of Health (NIH)
Institute
National Center for Research Resources (NCRR)
Type
Biotechnology Resource Grants (P41)
Project #
5P41RR006892-08
Application #
6282747
Study Section
Project Start
1998-05-05
Project End
1999-05-04
Budget Start
1997-10-01
Budget End
1998-09-30
Support Year
8
Fiscal Year
1998
Total Cost
Indirect Cost
Name
Columbia University (N.Y.)
Department
Type
DUNS #
064931884
City
New York
State
NY
Country
United States
Zip Code
10027
Halgren, Thomas A; Murphy, Robert B; Friesner, Richard A et al. (2004) Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. J Med Chem 47:1750-9
Friesner, Richard A; Banks, Jay L; Murphy, Robert B et al. (2004) Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem 47:1739-49
Baik, Mu-Hyun; Friesner, Richard A; Lippard, Stephen J (2003) Theoretical study of cisplatin binding to purine bases: why does cisplatin prefer guanine over adenine? J Am Chem Soc 125:14082-92
An, Yuling; Friesner, Richard A (2002) A novel fold recognition method using composite predicted secondary structures. Proteins 48:352-66
Gallicchio, Emilio; Zhang, Linda Yu; Levy, Ronald M (2002) The SGB/NP hydration free energy model based on the surface generalized born solvent reaction field and novel nonpolar hydration free energy estimators. J Comput Chem 23:517-29
Baik, Mu-Hyun; Friesner, Richard A; Lippard, Stephen J (2002) Theoretical study on the stability of N-glycosyl bonds: why does N7-platination not promote depurination? J Am Chem Soc 124:4495-503
Friesner, R A; Dunietz, B D (2001) Large-scale ab initio quantum chemical calculations on biological systems. Acc Chem Res 34:351-8
Gherman, B F; Dunietz, B D; Whittington, D A et al. (2001) Activation of the C-H bond of methane by intermediate Q of methane monooxygenase: a theoretical study. J Am Chem Soc 123:3836-7
Standley, D M; Eyrich, V A; An, Y et al. (2001) Protein structure prediction using a combination of sequence-based alignment, constrained energy minimization, and structural alignment. Proteins Suppl 5:133-9
Eyrich, V A; Standley, D M; Friesner, R A (1999) Prediction of protein tertiary structure to low resolution: performance for a large and structurally diverse test set. J Mol Biol 288:725-42

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