VMD-L Mailing List

From: Gumbart, JC (gumbart_at_physics.gatech.edu)
Date: Mon Feb 15 2021 - 09:55:07 CST

Hi Harper,

I think most people doing parameterization these days use dihedral scans. FFTK also sets an energy cutoff for fitting purposes (about 8-10 kcal/mol by default as I recall). Can’t you just fit the part before clashes increase the energy significantly?

Best,
JC

On Feb 11, 2021, at 7:30 PM, Smith, Harper E. <smith.12510_at_buckeyemail.osu.edu<mailto:smith.12510_at_buckeyemail.osu.edu>> wrote:

Hi all,

I am trying to use ffTK to parameterize a connection between two relatively rigid groups (a ribose and a guanidinium group). I don't think I can remove anything else from the system -- it's already as basic as possible. In the dihedral scanning portion, there are big clashes and they cause large energies in the MM portion. If I keep kmax at 3.0, the smallest RMSE I can get is around 60.

The ffTK paper mentions that estimates for dihedral force constants can come from vibrational analysis. Is this the best option for a system like mine? If so, could someone describe what this calculation would entail? ffTK has been an introduction to QM calculations for me, so any details or suggestions will be helpful!

Best,
Harper Smith