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; Altoè, P.; Bottoni, Andrea; Garavelli, Marco. - STAMPA. - 963:(2007), pp. 714-716. (Intervento presentato al convegno International Conference on Computational Methods in Science and Engineering 2007 (ICCMSE 2007) tenutosi a Corfu (Greece) nel 25–30 SEPTEMBER 2007) [10.1063/1.2836188].
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).I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.