Interface to the AMBER molecular dynamics package (http://ambermd.org, commercial software). It provides MM calculations using the AMBER family of forcefields.
Besides performing the MM calculations, the interface also handles the preparation of the calculation from a PDB file. The PDB file must be in a format recognized by AMBER and if it contains residues not included in the forcefield, additional parameter files have to be provided.
In latest versions of AMBER, the names of the leaprc files distributed as a part of the AMBERTOLLS package changes, and some of them were moved to a directort 'oldff'. Therefore, some of the examples provided here may need to be edited (as suggested in the comments) in order to run.
The AMBER interface supports the native_opt protocol which allows offloading a geometry optimization to AMBER.
In addition to complete optimization, it is possible to optimize or anneal only hydrogens. This is controlled by the keyword amber_opt_mode. Convergence limit, number of steps and some setup for the annealing can be controlled directly from cuby – see the list of keywords below.
The interface supports a range of implicit solvent models implemented in AMBER. There are multiple versions of the Generalized Born model (GBM and IGBx), and the Poisson-Boltzmann model (PB). For each model, the corresponding radii are written to the prmtop file.
By default, only the electrostatic contribution (dielectric screening) is calculated, the non-polar terms can be added using the keywords amber_gbsa and amber_pbsa for GB and PB models, respectively.