A QM-MM interface between CHARMM and TURBOMOLE: implementation and application to systems in bulk phase and biologically active systems.
The implementation of a hybrid QM-MM approach combining ab initio and density functional methods of TURBOMOLE with the molecular mechanics program package CHARMM is described. An interface has been created to allow data exchange between the two applications. With this method the efficient multiprocessor capabilities of TURBOMOLE can be utilized with CHARMM running as a single processor application. Therefore, features of nonparallel running code in CHARMM like the TRAVEL module for locating saddle points or VIBRAN for the calculation of second derivatives can be exploited by running the CPU intensive QM calculations in parallel. To test the methodology, several small systems are studied with both Hartree-Fock and density functional methods and varying QM-MM boundaries. Also, the computationally efficient RI-J method has been examined for use in QM-MM applications. A B(12) cofactor containing cobalt has been studied, to examine systems with a large QM region and transition metals. All tested methods perform satisfactory in comparison with pure quantum calculations. Additionally, algorithms for the characterization of saddle points have been tested for their potential use in QM-MM problems. The TRAVEL module of CHARMM has been applied to the Menshutkin reaction in the condensed phase, and a saddle point was located. This saddle point was verified by calculation of a steepest descent path connecting educt, transition state, and product, and by calculation of vibrational modes.
Loferer
Markus J
MJ
Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria.
Loeffler
Hannes H
HH
Liedl
Klaus R
KR
D003038:Cobamides / Q000737:chemistry; D008274:Magnesium / Q000737:chemistry; D008433:Mathematics; D008958:Models, Molecular; D008968:Molecular Conformation; D015394:Molecular Structure; D013816:Thermodynamics
D003038:Cobamides; D008274:Magnesium