Hello,
I am currently working on force field development for a modified DNA
structure and I'm trying to get a handle on the force field implementation
in AMBER. For testing purposes I have been sampling energies from the N3-H3
bond in a terminated DTN residue. Following is my procedure:
1. I have generated the DTN Structure by placing the terminating OH
hydrogen at (0,0,0) and importing the structure into tleap (all atoms are
automatically added).
2. The BSC1 forcefield was applied to generate topology and coordinate
files
3. From this structure the N3-H3 bond was stretched and contracted using
PyTraj
4. I have used both the PyTraj/libsander interface and a simple 1-step
minimization to confirm the energies at each step:
1-step energy
&cntrl
imin = 1,
maxcyc = 1,
ncyc = 1,
ntb = 0,
ntr = 0,
cut = 9999
/
- *Note: this was also confirmed using the parm98 forcefield built into
the Gaussian DFT package, which gave very similar values*
5. Finally, I plotted the energies from this and compared to the sum
of the following energies based on manually calculating the N3-H3
interaction by itself using BSC1 parameters:
- Coulomb energies (using qN3 = -0.434, qH3 = 0.342)
- Bonded energies (using k = 434 kcal mol^-1 Angstrom^-2 and r0 =
1.010)
- Lennard Jones energies (using rmin = 0.5*(1.8240 +1.1870) Angstroms
and eps = sqrt(0.1700*0.0157) kcal mol^-1 based on the mixing rules from
the manual)
- These parameters can be found on line 974 and 993 of parm10.dat
I have found that the energies I get from AMBER match up well for the
bonded energy curve, but the Lennard Jones curve I calculate causes a huge
energy rise at lower N3-H3 bond lengths that doesn't show up in the
calculations. This increase in energy from the LJ/VDW energy happens to
match up with the trend of DFT energies at those same bond lengths. Am I
missing a key parameter in AMBER that accounts for this difference or am I
calculating the Lennard Jones parameters incorrectly? Or perhaps there is
another better way to sample the energy from a force field?
Regards,
Will
--
William Livernois
Dept. Electrical and Computer Engineering
Email: willll.uw.edu
Phone: 813-323-1920
Pronouns: he/him/his
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Received on Mon Mar 25 2024 - 13:30:03 PDT
