CHARMM energy

Initial structures were refined against both the experimental restraints and the CHARMM energy using a novel simulated annealing protocol to define the torsion angle solutions to within an error of about 5°. Forty refined structures were used to obtain an average structure which was then further refined. A dielectric constant of 1 was used in the calculations. 

Figure 3.4 Comparison of CHARMM energy components vs. quantum mechanical values from SAPT2/jun-cc-pVDZ for the parallel-displaced benzene dimer at various horizontal displacements R and a fixed vertical displacement of 3.4 A (data from Sherrill et al. (2009a)). Solid lines are SAPT...

Bernhard R. Brooks, Robert E. Bruccoleri, Barry D. Olafson, David J. States, S. Swaminathan, and Martin Karplus. CHARMM A program for macro-molecular energy, minimization, and dynamics calculations. J. Comp. Chem., 4(2) 187-217, 1983. 

Brooks, B.R. Bruccoleri, R.E. Olafson, B.D. States, D.J. Swaminathan, S. Karpins, M. CHARMM A program for macromolecular energy, minimization, and dynamics calculations J. Comput. Chem. 4 187-217, 1983. 

Of the biomolecular force fields, AMBER [21] is considered to be transferable, whereas academic CHARMM [20] is not transferable. Considering the simplistic form of the potential energy functions used in these force fields, the extent of transferability should be considered to be minimal, as has been shown recently [52]. As stated above, the user should perform suitable tests on any novel compounds to ensure that the force field is treating the systems of interest with sufficient accuracy. 

This term is essential to obtain the correct geometry, because there is no Pauli repulsion between quantum and classical atoms. The molecular mechanics energy tenn, E , is calculated with the standard potential energy term from CHARMM [48], AMBER [49], or GROMOS [50], for example. 

The chemical reaction catalyzed by triosephosphate isomerase (TIM) was the first application of the QM-MM method in CHARMM to the smdy of enzyme catalysis [26]. The study calculated an energy pathway for the reaction in the enzyme and decomposed the energetics into specific contributions from each of the residues of the enzyme. TIM catalyzes the interconversion of dihydroxyacetone phosphate (DHAP) and D-glyceraldehyde 3-phosphate (GAP) as part of the glycolytic pathway. Extensive experimental studies have been performed on TIM, and it has been proposed that Glu-165 acts as a base for deprotonation of DHAP and that His-95 acts as an acid to protonate the carbonyl oxygen of DHAP, forming an enediolate (see Fig. 3) [58]. 

The energy functions for folding simulations include atom-based potentials from molecular mechanics packages [164] such as CHARMM [81], AMBER [165], and ECEPP... 

AD MacKerell Jr, B Brooks, CL Brooks III, L Nilsson, B Roux, Y Won, M Karplus. CHARMM The energy function and its paramerization with an overview of the program. In PvR Schleyer, NL Alhnger, T Clark, J Gasteiger, PA Kollman, HP Schaefer III, PR Schreiner, eds. Encyclopedia of Computational Chemistry, Vol 1. Chichester, UK Wiley, 1998, pp 271-277. 

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