This repository contains tabulated corrections for DFTB/DFTB2 and AM1/d-PhoT taken from the paper by Huang et al, 2014
Original tables have been extracted from supporting tables S1 and S2 of that paper.
External potentials in a format that can be read by PLUMED are provided.
A sample input file for PLUMED is also provided.
Implementation have been made by Alejandro Gil-Ley, Vojtech Mlynsky, and Giovanni Bussi
USE AT YOUR OWN RISK!
Usage:
> ./generate-grids.sh method sequence
Here methods is dftb3 or am1d,
and sequence is space separated sequence.
Example:
> ./generate-grids.sh dftb3 C G U U C G G C > plumed.dat
This will generate a plumed.dat input file as well as 8 grid files
containing the correcting potentials for the 8 nucleotides.
- Potential outside of the -pi/6,+pi/6 range for both Zx and Zy is set to an arbitrary value. Usually these variables should not reach the boundaries. In case they do it, one should set a wall to avoid it.
- Atom selection uses PLUMED MOLINFO syntax. Please double check that atoms for puckering have been properly selected.