positive Lennard-Jones energies

Jane Caldwell jane at NMRFAM.WISC.EDU
Wed Aug 14 15:20:53 EST 1996

Fellow X-PLOR users--

I've been calculating structures from NMR data and have
discovered that all my structures have positive values for
the Lennard-Jones energy.  This is surprising to me, 
since all of the other statistics look relatively good--
rmsd's are low, all the other energy terms are reasonably
small, and no constraints or bond lengths or angles
are violated consistently.  

The structures were calculated with distance geometry and refined
using the parallhdg.pro force field and the refine.inp protocol
(which uses a purely repulsive (REPEL) van der Waal's term).
I then transferred the structures to the PARAM19x and PARALLH22X
force fields and calculated the Lennard-Jones energies with the
TRUNCated potential and cutnb=50.  Both force fields gave me
values greater than zero, ranging from 100-200 and 1000-3000
kcal/mol, respectively.

Has anyone else run into similar problems?  If anyone has
suggestions or strategies for identifying the problem, I'd
be grateful--



Jane Caldwell
Biophysics Program/Dept. Biochemistry
420 Henry Mall
University of Wisconsin-Madison
Madison, WI 53706

E-mail: jane at nmrfam.wisc.edu

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