Software and Data

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Endo S2: Files for performing MD simulations
Utilities for base stacking calculations
Charge and polarizability prediction for Drude FF

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.

FFParam: A Standalone Package for CHARMM Additive and Drude Polarizable Force Field Parametrization of Small Molecules

FFParam is a python package with GUI for parametrization of small molecules. It supports both the CGenFF/CHARMM Additive and Drude Polarizable Force-Fields.

FFParam v1.0.0

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.

Download link

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.


Endo S2: Files for performing MD simulations

Input files to perform the 16 microsecond+ MD simulations and final snapshots from the simulations. See the .rtf file for more information.

Aytenfisu, A.H., Deredge, D., Klontz, E.H., Du, J., Sundberg, E., and MacKerell, Jr., A.D. "'Insights into substrate recognition and specificity for IgG by Endoglycosidase S2" PLoS Computational Biology, Under review, 2021, [DOI]

See the .rtf file in the .zip package for a description of the contents.

Download .zip file containing input scripts and data files