Hi AMBER users,
I have a question regarding the assignment of GAFF2 parameters
(gaff2.dat, Version 2.1, April 2016) to the dihedral angle c3-c3-os-c3.
For this dihedral angle, the gaff2.dat file lists the following lines:
X -c3-os-X 3 1.150 0.000 3.000
JCC,7,(1986),230
c3-os-c3-c3 1 0.240 0.000 -3 p29 GA
AUE=0.4256 RMSE=0.5201 TorType=2
c3-os-c3-c3 1 0.160 0.000 2 p29 GA
AUE=0.4256 RMSE=0.5201 TorType=2
c3-c3-os-c3 1 0.910 0.000 -3
lactose1,ccoc GA AUE=1.5236 RMSE=2.4206 TorType=3
c3-c3-os-c3 1 1.000 0.000 -2
c3-c3-os-c3 1 0.000 0.000 1
Of course the fist line has to be omitted, since there are explicit
entries for c3-c3-os-c3/c3-os-c3-c3. However, the .frcmod file prepared
by parmchk2 lists the following lines:
c3-c3-os-c3 1 0.240 0.000 -3.000
c3-c3-os-c3 1 0.160 0.000 2.000
c3-c3-os-c3 1 1.000 0.000 -2.000
c3-c3-os-c3 1 0.000 0.000 1.000
Finally, the .prmtop file prepared by leap contains only the values of
theses lines:
c3-c3-os-c3 1 0.240 0.000 -3.000
c3-c3-os-c3 1 0.160 0.000 2.000
c3-c3-os-c3 1 0.000 0.000 1.000
Why is the line (1/0.910/0.000/2) missing in .frcmod? How (and why) do
antechamber/leap choose the final values for the .prmtop file and not
the lines (1/0.910/0.000/-3 1/1.000/0.000/-2) instead?
Best regards
Johannes Träg
P.S. I'm using AmberTools 16
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Received on Fri Mar 15 2019 - 08:30:04 PDT
