Software and Data
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Charge and polarizability perdiction for Drude FF
Utilities for base stacking calculations
HREX trajectories from the Klebsiella pneumoniae lipopolysaccharide study
Given below are various scripts, software packages and data that we have developed and are making publicly available. For anything related to force field development, please see our Force Field Development page.
Charge and polarizabilites prediction tool for the Drude Force Field
Heid, E., Fleck, M., Chatterjee, P., Schröder, C., and , MacKerell, Jr., A.D. "Towards Prediction of Electrostatic Parameters for Force Fields that Explicitly Treat Electronic Polarization," Journal of Chemical Theory and Computation Submitted, 2019.
Download bash and python scripts to predict partial atomic charges and atomic polarizabilities for the Drude Force Field. Input for the prediction tool is the CGenFF toppar stream file of the molecule that contains both the topology and parameter information generated using the CGenFF program or with the PARAMCHEM server.
The DIRECT-ID method computes norm difference matrices from covariance matrices routinely computed after MD simulations. The norm surfaces can be used to (1) quantify the extent of difference in the dynamics and (2) extract structurally relevant features that contribute most prominently to the dynamics. These differences can be a function of solution conditions, ligand binding, etc.
Please cite the following article if you use DIRECT-ID in your research:
S.K. Lakkaraju, J.A. Lemkul, J. Huang, and A.D. MacKerell, Jr. (2016) "DIRECT-ID: An Automated Method to Identify and Quantify Conformational Variations - Application to β2-adrenergic GPCR." J. Comput Chem. 37: 416-425. DOI:10.1002/jcc.24231
Example scripts for determination of intermolecular orientation and generation of Z-matrices for QM optimization of stacked base monomers
McDonald, A.R. Denning, E.J. and MacKerell, Jr. A.D. "Impact of Geometry Optimization on Base-Base Stacking Interaction Energies in the Canonical A- and B-Forms of DNA," Journal of Physical Chemistry A 117: 1560-1568, 2013.