Hi Dr. Case and Dr. Wang,
In addition to c3-c3-os-c3, there’re 2 other torsion that have parameters that seem inconsistent, see the following. Could you clarify which parameters should be used or if I’m misinterpreting the parameters? Thank you!
1)
c2-ce-ca-ca 1 0.505 180.000 2 add6f SS AUE=0.2273 RMSE=0.3302 TorType=3
ca-ca-ce-c2 1 0.618 180.000 2 c24 SS AUE=0.2364 RMSE=0.3330 TorType=3
2)
c -n -c3-c3 1 0.100 180.000 -4 p19 GA AUE=0.2882 RMSE=0.4031 TorType=2
c -n -c3-c3 1 0.170 0.000 -3 p19 GA AUE=0.2882 RMSE=0.4031 TorType=2
c -n -c3-c3 1 1.020 180.000 1 p19 GA AUE=0.2882 RMSE=0.4031 TorType=2
c3-c3-n -c 1 0.650 180.000 -4 sialic2 GA AUE=1.1541 RMSE=1.2847 TorType=3
c3-c3-n -c 1 0.030 180.000 -3 sialic2 GA AUE=1.1541 RMSE=1.2847 TorType=3
c3-c3-n -c 1 2.260 0.000 1 sialic2 GA AUE=1.1541 RMSE=1.2847 TorType=3
In addition to that, the following torsion also has two parameters, but they’re the same, so whichever parameter is used is fine.
hc-c3-c3-c3 1 0.080 0.000 3 m2 SS AUE=0.2468 RMSE=0.2989 TorType=2
c3-c3-c3-hc 1 0.080 0.000 3 t2 SS AUE=0.2507 RMSE=0.3027 TorType=3
Best,
Lin
On Aug 5, 2019, at 9:27 PM, David Case <david.case.rutgers.edu<mailto:david.case.rutgers.edu>> wrote:
On Mon, Aug 05, 2019, Lin Song wrote:
May I ask if you have figured out which lines should be used as the
c3-c3-os-c3 torsion parameter? I’m confused about this as well. It seems
to me there’re two sets of parameters excluding the first line, one is
for TorType=2, the other is for TorType=3. Could you also explain what
does the TorType mean?
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.
c3-os-c3-c3 1 0.240 0.000 -3 p29 GA
c3-os-c3-c3 1 0.160 0.000 2 p29 GA
c3-c3-os-c3 1 0.910 0.000 -3
c3-c3-os-c3 1 1.000 0.000 -2
c3-c3-os-c3 1 0.000 0.000 1
cc-ing (again?) to Junmei: it certainly looks like there are
inconsistent parameters in gaff2.dat for this particular torsion. Can
you clarify what should be used? (Or perhaps I'm misinterpreting
something here....)
....dac
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Received on Fri Aug 09 2019 - 09:00:02 PDT
