parameter file energy constant and equilibrium values

Gerard "CD" Kleywegt gerard at
Mon Nov 1 12:54:50 EST 1999

check which dihedrals are restrained even though they
shouldn't be in your opinion; then edit the topology
file and comment out the corresponding DIHEdral statements
(by putting an exclamation mark in front of each)

it may be that there are some dihedrals which accidentally
are close to "too good to be a coincidence" values (such
as 0 or 180), and which therefore will engender a DIHEdral
restraint in XPLO2D


On 29 Oct 1999, Robert D. Scavetta wrote:

> 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.
> Thanks,
> Robert
> -- 
> 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

                        Gerard J.  Kleywegt
Dept. of Cell & Molecular Biology  Bolshewik University of Uppsala
                Biomedical Centre  Box 596
                SE-751 24 Uppsala  SWEDEN  mailto:gerard at
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.


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