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Scheraga, "A comparison of the CHARMM, AMBER and ECEPP potentials for peptides.
Development and current status of the CHARMM force field for nucleic acids.
For the minimization, the CHARMM v27 force field was used with the conjugate gradient minimization scheme.
et al., "CHARMM: the biomolecular simulation program," Journal of Computational Chemistry, vol.
For obtaining topology file and parameters of small compounds, we employed SwissParam to generate these data and compatible with the CHARMM all atoms force field for GROMACS simulation.
The minimization protocol employed the steepest descent method using BIO+, the HyperChem implementation of CHARMM (Chemistry at HARvard using Molecular Mechanics) force field (18), until the difference in energy after two consecutive iterations was less than 0.1 kcal/mol.
The structural analysis of the proteins was done using Accelry's Discovery Studio [19] with 'smart minimizer' and CHARMm force field.
By using CHARMM, a molecular dynamics software, we performed a computer simulation of the protein Cyt1A from Bacillus thuringiensis var.
ChemSketch also features molecular modelling applications which allow for 3-D rotation and for 3-D optimization of the structure using CHARMM parameterization.
[1994] for the widely used molecular mechanics and dynamics program CHARMM and was shown to be an efficient tool for the minimization of molecular potential functions in comparison to other available minimizers.
Examples include DYNA-3D and PRONTO-3D for structural mechanics modeling, GAUSSIAN and DMOL for quantum mechanical simulation of molecules, CHARMM and DISCOVER for molecular dynamics simulation for organic systems, and FIDAP for modeling complex fluid flows.