Rapid and accurate parameterization of new molecules in CHARMM

From: Aaron Larsen (alarsen_at_molbio.mgh.harvard.edu)
Date: Tue May 27 2014 - 08:21:06 CDT


I'm quite interested in doing a large number of MD simulations on a host of
highly similar molecules (nucelobases mostly) that are not well
parameterized in any force field that I am aware of. I would appreciate a
suggestion on what tools and strategies would be best suited for the rapid
paramaterization of multiple molecules in CHARMM. Maximum automation is a
high priority as manually entering atom types for 100+ molecules seems
rather dull. If possible, I would like to avoid software with paid academic
licenses, so that might preclude Gaussian.


Aaron Larsen, Ph.D.
Harvard University Department of Chemistry and Chemical Biology
Harvard Medical School Department of Genetics
E-mail: alarsen_at_molbio.mgh.harvard.edu
Mobile: 617-319-3782
FAX: 617-643-3328

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