Questions and problems?
Prep, negative sign
I have a simple question about the diagnotic output of PREP.
What is the meaning of the '-' sign before the atom number in the
list of dihedrals. For instance,
1 -1 3 1 -2
or
13 8 27 -29 11
Torsion angles with a negative value in the fourth column refer to
torsions for which 1-4 non-bonded interactions should not be calculated
(because, e.g., the torsion is within a five membered ring, where the
endpoints of the torsion will also be separated by only one bond);
Torsion angles with a negative value in the fifth colum refer to
"improper" torsions, as defined in the prep file (1-4's are not
calculated for these torsions, either).
I guess it can be a bit bewildering to find these negative values in
the output with no explanation. That said, there is probably no reason
that you, as the end-user, would ever be concerned with their actual
meaning!
dap
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Last modified: Tue Nov 15 18:50:24 1994