Dear Dr. Gale,
I was trying to understand how the GAFF force field was defined in the gaff.lib file (at gulp-6.1.2/Libraries/).
Two questions came up:
why in the section “epsilon kcal” every sigma (in fact r_min) value is multiplied by 2?
Amber uses the r_min notation, which is the same used by GULP once “lennard epsilon geometric 12 6 x13 kcal all 0.5 12.0” is defined.
I don’t understand this explanation:
“# NNB: In Amber one of two improper torsions is chosen whereas in GULP both improper angles are used but the force constant is halved.”
I was looking in both AMBER and GULP manuals and could not find the reason for dividing by 2 the force constant of the improper torsions.