Re: Rapid and accurate parameterization of new molecules in CHARMM

From: Aaron Larsen (
Date: Tue May 27 2014 - 19:22:22 CDT

"There aren't 100+ common nucleobases in nature."

I'd like to evaluate many small hypothetical modifications. GAAMP would be
great but they tell me that I don't have authorization to get the necessary
passcode, which is a shame. As far as I am aware the ffTK also requires the
use of Gaussian for geometry optimization/water interaction/charge
optimization etc. steps.

As it turns out, my lab does have access to Gaussian, so this may not be a
limitation any longer but if there's a way that smaller changes can be
evaluated in a more automated fashion, I'm all ears!


On Tue, May 27, 2014 at 7:11 PM, Kenno Vanommeslaeghe <> wrote:

> 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...

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

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