Re: Rapid and accurate parameterization of new molecules in CHARMM

From: Kenno Vanommeslaeghe (
Date: Tue May 27 2014 - 17:58:42 CDT

On 05/27/2014 10:19 AM, JC Gumbart wrote:
> If you want to err on the side of speed, then something like ParamChem
> might work: 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.

Very good advice. Though in the original question, "nucelobases mostly"
and "100+, not well parameterized in any force field" are at odds. There
aren't 100+ common nucleobases in nature. The ones that are are well
supported by the CHARMM Nucleic Acid (NA) force field, and modest
modifications may be performed with ffTK (or GAAMP). But if you're talking
about bigger changes, you're quickly drifting outside the coverage of the
NA FF and into the realm of general heterocycles, which are better covered
by CGenFF. In that case, the recommendation would be to first get an
initial guess from , then refine it with ffTK (or GAAMP)
where necessary.

> However, it does presently rely on Gaussian, so if you don’t have access
> anywhere, you might be out of luck.

Q-Chem now has relaxed PES capability. We've been planning to make a
Q-Chem variant of our procedure, which we could then present to the ffTK
developers, but there are always more pressing things getting in the way.
Of course Q-Chem, just like Gaussian, is commercial software...

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