Dear Amber Experts,
I have a question about the main parameter sets in Amber, specifically, gaff2.dat and parm10.dat. I was checking these files and trying to get a sense of the force constant of an improper dihedral, for example, the improper torsion in a carboxylate group C(=O)O.
In gaff2.dat, the improper section begins with:
X -o -c -o 1.1 180. 2. JCC,7,(1986),230
X -X -c -o 10.5 180. 2. JCC,7,(1986),230
However, in parm10.dat I saw…
X -X -C -O 10.5 180. 2. JCC,7,(1986),230
X -O2-C -O2 10.5 180. 2. JCC,7,(1986),230
My question is: In which order do dihedral types override?
Will X -o -c -o eventually get overridden by X -X -c -o, because X -X -c -o appears after it? Or is there some priority rule, according to number of wildcards that are required to match?
Ps. On the referenced paper (
https://doi.org/10.1002/jcc.540070216), both got a force constant = 10.5. But I understand if it was modified for particular reason like to balance with the other GAFF parameters. I was just curious if I need to reuse the GAFF parameters for validation purposes, which should I choose? 1.1 or 10.5?
Thank you for your time and kind advice in advance!
Many Thanks,
--
Amy He
Chemistry Graduate Teaching Assistant
Hadad Lab
Ohio State University
he.1768.osu.edu<mailto:he.1768.osu.edu>
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Received on Sun Nov 12 2023 - 02:00:01 PST
