From: Tristan Croll (tristan.croll_at_qut.edu.au)
Date: Tue May 27 2014 - 17:23:07 CDT
If you’re willing to switch to the GROMOS force field, there’s an ab initio server at http://compbio.biosci.uq.edu.au/atb/index.py?tab=home_tab&nocache=470. You’d have to talk to the owners about submitting a large set, though.
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf Of JC Gumbart
Sent: Wednesday, 28 May 2014 12:20 AM
To: 'Aaron Larsen'; namd-l_at_ks.uiuc.edu
Subject: RE: namd-l: Rapid and accurate parameterization of new molecules in CHARMM
Your two goals are slightly at odds with each other (rapid and accurate). If you want to err on the side of speed, then something like ParamChem might work: https://cgenff.paramchem.org/ It should be noted, however, that since nucleobases are already in the charmm36 force field, using ParamChem (which pulls from the CGenFF) is going to be far from ideal.
For increased accuracy, you can turn to the Force Field Toolkit in VMD to determine those parameters not already present in C36: http://www.ks.uiuc.edu/Research/vmd/plugins/fftk/
However, it does presently rely on Gaussian, so if you don’t have access anywhere, you might be out of luck.
A final option that might split the difference for you (web-based, but still includes ab initio calculations) is GAAMP: http://gaamp.lcrc.anl.gov/
Nonetheless, I don’t think any option you find will be fully automated.
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf Of Aaron Larsen
Sent: Tuesday, May 27, 2014 9:21 AM
Subject: namd-l: Rapid and accurate parameterization of new molecules in CHARMM
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
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