parameter file energy constant and equilibrium values

Robert D. Scavetta robert.scavetta at UCHSC.EDU
Fri Oct 29 11:58:09 EST 1999

Hi all,

I am trying to model S-adenosylmethionine (AdoMet) into my electron
density.  I generated the parameter and topology files that were
produced by xplo2d and made some corrections to the file.  The adenine
moiety of AdoMet is behaving very well, but the methionine and ribose
moieties do not behave well when I run CNS.  The ribose will not alter
its ring pucker geometry to fit the electron density even after manually
altering the ring pucker in O.  When I run CNS, the ring converts back
to its previous geometry.  The Methionine moiety also refuses to alter
its conformation about several bonds.

What am I doing wrong?  

What energy constants or equilibruim values in the parameter file do I
have to alter?  

Do I have to alter anything in the topology file?

Any and all help would be appreciated.


Robert Scavetta				robert.scavetta at
Department of Pharmacology, C236
University of Colorado Health Sciences Center
4200 E. 9th Avenue
Denver, CO  80262

(303) 315-8044
(303) 315-6464
(303) 315-7097  fax

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