Re: [AMBER] leap mis-specified improper dihedral

From: FyD <>
Date: Wed, 21 Dec 2011 08:22:44 +0100

Bill, Dean, Dr Case,

>> > When I ran xleap, I obtain an improper that is (Y-X-Y-Y) where all the
>> > atoms are correct, except the sp2 center is in the second position of the
>> > specified dihedral.
>> This is OK: a dihedral angle is unchanged when you reverse the order of the
>> atoms.
> I remember deciding with Prof Kollman that the center atom should
> always be in the 3rd place. Since impropers should always be planar
> (since one can't depend on the sense of the cases with a duplicate
> atom type), perhaps it doesn't matter.

If I remember well an improper was rigorously defined in plep; i.e.
the conventions for an improper torsion named A–B–‘C’–D were that the
out of plane center was listed in the third position and the order of
the other three was determined alphabetically by atom type, and by
atom number (i.e., their order in the molecule) when atom types were
identical. But the later conventions were lost in LEaP...

regards, Francois

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Received on Tue Dec 20 2011 - 23:30:03 PST
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