Science Buddies: "Ask an Expert"

Hello! I am trying to understand the General Amber Force Field (GAFF) located at http://archive.ambermd.org/201111/att-0689/gaff.dat. The gaff.dat file doesn't come with much documentation, so I have several questions to ask!

In OpenBabel, torsion terms seem to be defined in the format (excerpt):
X -c -c -X 4 1.200 180.000 2.000
X -c -c1-X 2 0.000 180.000 2.000
X -c -cg-X 2 0.000 180.000 2.000 same as X-c-c1-X
X -c -ch-X 2 0.000 180.000 2.000
X -c -c2-X 4 8.700 180.000 2.000 intrpol.bsd.on C6H6

Where the first column are the 4 atoms in the torsion chain.

1. OpenBabel computes some value vn_half by dividing the third column by the second column, then converting to Kilojoules. This is out of curiosity, but what values do the second and third columns represent?


Also, as I move down the list of torsions I get to a line break and see the format change slightly (excerpt):

X -o -c -o 1.1 180. 2. JCC,7,(1986),230
X -X -c -o 10.5 180. 2. JCC,7,(1986),230
X -X -ca-ha 1.1 180. 2. bsd.on C6H6 nmodes
X -X -n -hn 1.1 180. 2. JCC,7,(1986),230
X -X -n2-hn 1.1 180. 2. JCC,7,(1986),230
X -X -na-hn 1.1 180. 2. JCC,7,(1986),230
X -c3-n -c3 1.1 180. 2. JCC,7,(1986),230

2. Are these the improper torsion definitions?


Furthermore, I noticed that there are duplicate atom-groups with different params (excerpt):
c3-c3-c3-c3 1 0.18 0.0 -3. Junmei et al, 1999
c3-c3-c3-c3 1 0.25 180.0 -2. Junmei et al, 1999
c3-c3-c3-c3 1 0.20 180.0 1. Junmei et al, 1999

When given a torsion with 4 c3 molecules, how do I know which one to use?

Thanks!

- Eric

Hello ericjang,

A file with an extension of .dat could contain almost anything. One cannot even deduce what sort of data it contains unless it has some documentation inside. You can make a questionable guess that it contains "data".

Your best bet to understand this file and the details of the AMBER "force field" calculation is the http://ambermd.org/ web site. See my notes in replying to your other post for how to go about this search.

Good luck, WW