Software
Alchemify: An X-PLOR PSF post-processor for alchemical free-energy calculations in NAMD. Alchemify is a small program that handles nonbonded exclusion lists and remove unwanted bonded terms, which appear in the definition of hybrid dual topologies.
Novel free-energy developments in NAMD are reported on the web site of the Theoretical and Computational Biophysics Group at the University of Illinois, Urbana-Champaign. Specific information about the adaptive biasing force method can be found on the ABF website.
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- Molefacture: The Molefacture plugin provides VMD users with an interface to edit molecules. This includes the ability to add, delete, or manipulate their structure at an atomic level, and to build new components from a library of common fragments. It also offers a front-end for the setup of alchemical free-energy perturbation calculations. - ParseFEP: ParseFEP consists of a set of tools for the analysis of free-energy perturbation calculations carried out within NAMD. - Mutator: Mutator is a tool for mutating a target residue selected by its segment name and id, and the three character residue code for the mutant amino acid. It can also build, for the specific purpose of alchemical free-energy calculations, a hybrid structure where both the initial and mutated side chains are present. It features a library of all possible amino-acid hybrid dual topologies.
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Optimally Partitioned Electric Properties: A tool for the derivation of models of distributed multipoles and polarizabilities. Using local frames of reference, OPEP determines distributed multipoles up to hexadecapoles from the molecular electrostatic potential, and distributed, isotropic or anisotropic polarizabilities up to quadrupolar from the induction energy mapped spatially around the molecule of interest.
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