Refine
Departments, institutes and facilities
Document Type
- Article (51)
- Conference Object (5)
- Part of a Book (2)
- Contribution to a Periodical (1)
- Patent (1)
Year of publication
Language
- English (60) (remove)
Has Fulltext
- no (60) (remove)
Keywords
- Force field (3)
- Software (2)
- ACPYPE (1)
- AMBER (1)
- Alkane (1)
- Atomistic force fields (1)
- Basis set (1)
- Binding Sites (1)
- Carbohydrate (1)
- Computational chemistry (1)
Herein we report an update to ACPYPE, a Python3 tool that now properly converts AMBER to GROMACS topologies for force fields that utilize nondefault and nonuniform 1–4 electrostatic and nonbonded scaling factors or negative dihedral force constants. Prior to this work, ACPYPE only converted AMBER topologies that used uniform, default 1–4 scaling factors and positive dihedral force constants. We demonstrate that the updated ACPYPE accurately transfers the GLYCAM06 force field from AMBER to GROMACS topology files, which employs non-uniform 1–4 scaling factors as well as negative dihedral force constants. Validation was performed using β-d-GlcNAc through gas-phase analysis of dihedral energy curves and probability density functions. The updated ACPYPE retains all of its original functionality, but now allows the simulation of complex glycomolecular systems in GROMACS using AMBER-originated force fields. ACPYPE is available for download at https://github.com/alanwilter/acpype.
The invention relates to compounds that include peptide and peptidomimetics that inhibit estrogen receptor dependent cell proliferation. The compounds of the invention are useful for treating cell proliferative disorders or physiological conditions characterized by undesirable or unwanted estrogen induced cell proliferation, including breast cancer.
Structure-activity relationships of thiostrepton derivatives: implications for rational drug design
(2014)
Liquid–liquid equilibria of dipropylene glycol dimethyl ether and water by molecular dynamics
(2011)
Computational chemistry began with the birth of computers in the mid 1900s, and its growth has been directly coupled to the technological advances made in computer science and high-performance computing. A popular goal within the field, be it Newtonian or quantum based methods, is the accurate modelling of physical forces and energetics through mathematics and algorithm design. Through reliable modelling of the underlying forces, molecular simulations frequently provide atomistic insights into macroscopic experimental observations.
Modeling of magic water clusters (H2O)20 and (H2O)21H+ with the PM3 quantum-mechanical method
(1993)
Reconciling solvent effects on rotamer populations in carbohydrates - A joint MD and NMR analysis
(2006)
NMR structures of thiostrepton derivatives for characterization of the ribosomal binding site
(2011)