WARNING: this is an archive page that mostly reflects my research activities at the University of Maryland, Baltimore up to the end of 2015. A notable exception is my CGenFF section, which is hosted on this site (mackerell.umaryland.edu) for the time being.

Click here for my (somewhat) updated home page at my current institution.

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Kenno Vanommeslaeghe
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MacKerell Lab
Computer-Aided Drug Design Center

University of Maryland, Baltimore

20 Penn Street
HSF-II Rm. 631
Baltimore, MD 21201

Manual parameter fitting: see the tutorial and the FAQ

Color graph of how bias affects a typical ill-conditioned pair of dihedrals, from 2015 least-squares parameter fitting paper

Automatic parameter fitting

Version 0.9.1 beta of the lsfitpar program for robust fitting of bonded parameters is available under the Affero GPL. The two most straightforward ways to obtain it are:

In both cases, this yields (among other things) a README file with further instructions. Also included in the repository is an examples subdirectory containing a tutorial that guides the reader through the practical aspects of bonded parameter fitting and the different features of the lsfitpar program, and a scripts subdirectory with handy helper scripts (the tutorial explains their usage). We hope this material will be helpful to your research, and appreciate feedback; see the e-mail link in the page header.

Reference: K. Vanommeslaeghe, M. Yang, A. D. MacKerell Jr., Robustness in the fitting of Molecular Mechanics parameters, J. Comput. Chem. 2015, 36, 1083-1101. DOI:10.1002/jcc.23897 .

This material is based upon work supported by the National Science Foundation under Grant No. 0823198. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.

Last updated Monday, the 8th of June 2015