Dear Amber Community,
I have been working on amber parameterization of a specific dihedral angle
(IDIVF=1) in a residue. I have initially determined RESP charges for the
small molecule. Then I determined PES about the torsion of interest by QM
(at MP2 level) and MM (for non-bonded potentials in gas phase). I replotted
the PES curves by referencing to their lowest minimum points (that is,
zeroed the lowest minimum points). I then substracted the plots (Eqm -
Emm). I also zeroed the lowest minimum point in the resulting plot, which
gave rise to four energy barriers (PN=4).
Using a Fourier series with a single cosine term I determined PHASE angles
for each energy barriers. Well, I did not deconvolute the difference PES
curve. Instead, I took half the max potential-energies at the barriers and
divided them by 6 (that is possible # of torsions about the torsion of
interest. Hope I did this right ! )
Here are the values I came up with:
IDIVF PK/6 PHASE PN
O-CT-N-C 1 0.382890 108.00 -1.
O-CT-N-C 1 2.767235 33.27 -2.
O-CT-N-C 1 4.160948 -250.41 -3.
O-CT-N-C 1 1.325341 78.46 4.
My questions are :
1) It has been more than 10 years since I last parameterized a torsion
angle right. To refresh my memory, Can an amber expert possibly confirm the
general steps (outlined above) I took to derive the dihedral parameters.
2) In line of PN = -3, PHASE = -250.41, a negative PHASE value, does not
sound right to me? Can it be replaced with (360 - 250.41 =) 109.59 ?
3) I have checked some amber FF parameters and I noticed some negative PK
values. What is the rationale for negative PK values as energy barriers
possess positive energies in difference PES curves after zeroing the lowest
minimum energy point?
Thanks in advance for enlightening me.
Best,
Cenk Andac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Feb 07 2022 - 13:30:02 PST
