This contribution illustrates some features of a new of a newly implemented general hybrid approach. This method, included in the COBRAMM (Computations at Bologna Relating Ab‐initio and Molecular Mechanic Methods) suite of programs, has a modular structure that integrates some specialized programs and represents a flexible computational environment that increases the flexibility/efficiency of QM, and MM, and QM/MM calculations. Here we describe some aspects of the geometry optimization procedure and explain some approximations used in the frequency computation. Moreover we present two analysis procedures that allow to rank the contribution of the various aminoacid residues of an enzyme in determining the catalytic mechanism and the shape of a Potential Energy Surface (PES).

COBRAMM (part 2): an Overview on Some Computational Details; Geometry Optimization, Frequency Calculation, Analysis of the Results

STENTA, MARCO;BOTTONI, ANDREA;GARAVELLI, MARCO
2007

Abstract

This contribution illustrates some features of a new of a newly implemented general hybrid approach. This method, included in the COBRAMM (Computations at Bologna Relating Ab‐initio and Molecular Mechanic Methods) suite of programs, has a modular structure that integrates some specialized programs and represents a flexible computational environment that increases the flexibility/efficiency of QM, and MM, and QM/MM calculations. Here we describe some aspects of the geometry optimization procedure and explain some approximations used in the frequency computation. Moreover we present two analysis procedures that allow to rank the contribution of the various aminoacid residues of an enzyme in determining the catalytic mechanism and the shape of a Potential Energy Surface (PES).
COMPUTATIONAL METHODS IN SCIENCE AND ENGINEERING: Theory and Computation: Old Problems and New Challenges. Lectures Presented at the International Conference on Computational Methods in Science and Engineering 2007 (ICCMSE 2007): VOLUME 1
714
716
Stenta, Marco; Altoè, P.; Bottoni, Andrea; Garavelli, Marco
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Utilizza questo identificativo per citare o creare un link a questo documento: http://hdl.handle.net/11585/59876
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