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

Hello,

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.

Best,
Aaron

-- 
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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