Hi all,
I have a model of a saccharide binding/catalyzing protein with substrate. I
have generated/created appropriate toph and param files to describe the monomer
unit of the substrate (galacturonic acid) and described the linkages between
monomer units based on the param and toph files for cho.
I have placed the monomer units into the e- density and ran it through x-plor.
X-plor has adjusted the sugar rings only slightly to try to conform the ring
to the density. The ring of the monomers are highly contorted and strained.
And x-plor appears not to be able to place the atoms of the ring properly into
the density.
How do I lighten up on the geometry constrants on the ring geometry to allow
x-plor to fit the ring to the density?
Do I lower the energy of the dihedrals or the impropers or what?
Do I issue a command in the x-plor input file that will ignore the geometry
information in the param and toph files for the carbohydrate?
Any and all advice is welcomed.
Thanks,
--
Robert D Scavetta
Department of Biochemistry
1447 Boyce Hall
University of California
Riverside, CA 92521
email: scavetta at xtreme.ucr.edu
phone: (909) 787-4196
fax: (909) 787-3590
