AMBER Archive (2008)

Subject: Re: AMBER: LEap error message for parmBSC0 force field

From: Bill Ross (
Date: Thu Apr 03 2008 - 15:12:12 CDT

> ** Warning: No sp2 improper torsion term for OS-H1-CI-CT
> atoms are: O5' H5'2 C5' C4'
> ** Warning: No sp2 improper torsion term for H1-H1-CI-CT
> atoms are: H5'1 H5'2 C5' C4'
> If I remember correctly, these messages appear whenever an atom has
> 3 neighbors and no improper term applies. It is suspicious that this
> is happening to C5' (the 3rd atom is the central one) - shouldn't it
> have 4 neighbors? (O5', H5'1, H5'2, C4') I.e. possibly in one or more
> places you are missing H5'1 and in other(s) a bond to O5'.

Other than that, it is not a problem to have impropers 'missing'
if you don't care about that set of 4 atoms being planar, or think
that other potentials will suffice to keep them planar.

Note that non-planar impropers are not handled by leap.

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