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Department of Chemistry and Chemical Biology |
Questions and problems?Prep, negative signI 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 -2or
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 Web Masters <webadmin@www.amber.ucsf.edu> Last modified: Tue Nov 15 18:50:24 1994 |
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