Will, if you're only moving the H3, then the vdw changes should just relate
to pairs involving the H3.
the MM force field doesn't include pairs for which the H3 is involved in a
bond or angle term with the other atom.
also, the "1-4" terms (3 bonds away) are scaled.
There are probably better ways to get the energy data for those structures,
such as using cpptraj. I also would consider that even 1 step of min will
change the structure when it is so highly strained.
and overall... I'm not sure that bonds the resulting info will be helpful.
the harmonic MM bond won't really match up to real QM data in any case.
are you trying to use the energies that you get, or just doing this to make
sure you understand the force field? My opinion would be that the
energies you get from bond stretching won't be useful. normally the
reference length and the force constant come from sources other than this
(like lengths from crystal structures, force constants from vibrational
frequencies).
On Mon, Mar 25, 2024 at 4:25 PM William Livernois via AMBER <
amber.ambermd.org> wrote:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Mar 25 2024 - 14:00:03 PDT
