halide toplogy and paramaters

Christine Gee c.gee at imb.uq.edu.au
Wed Nov 26 21:05:33 EST 2003


Hi
We have a structure where we are trying to model an inhibitor.  the
inhibitor has two chlorines (side by side) off a benzene ring.  The
Chlorines are not refining properly with our top and par files - there
is a big 3sigma fo-fc density around them telling us we are not
accounting for all the electrons there.  We have used par and top files
generated by the Hic-up and dundee prodrug programs and both gave
similar results.  Any suggestions as to which part of the parameter and
torsion files I should be concentrating on?  Or does anyone know of any
similar compounds with top and par files which are OK?  Or can anyone
tell me what the partial charges on the Cl and C molecules should be?
Thanks
Christine

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