I am trying to parameterize a molecule. I know dihedrals and impropers are the same for Amber Force Field. (Source: http://archive.ambermd.org/201004/0334.html) So, I did PET scan for improper and I found this chart:
According to this chart and Amber7 manual Appendix-C I should define impropers like this in my mini-force field:
C-O-B-C 40.5 180.0 2.0
But in gaff and gaff2 the biggest improper values are not greater than 15 ( here is gaff2: https://github.com/choderalab/ambermini/blob/master/share/amber/dat/leap/parm/gaff2.dat and here is gaff: https://github.com/choderalab/ambermini/blob/master/share/amber/dat/leap/parm/gaff2.dat)
And to compare my improper values with gaff, I scanned C-C-C-C impropers and I obtained almost the same chart as above but in gaff, this improper is defined like this:
C-C-C-C 1.1 180.0 2
so it is obvious gaff doesn't use PES scan values for improper but it seems unreasonable because dihedral values fits with PES scan. So what should I do? Should I use values which I obtained from PES scan ( C-O-B-C 40.5 180.0 2.0) or what should I do?