Hi Charles,
We are trying to dock two proteins using PRE data (sbmf mode). In the
calculation we are using three mtsl conformers
to represent each probe. The docking protocol works, but the the
calculated VDW energies are quite large. The structures look ok (no
protein overlap)
so I think the high energies are because the
analyze() function used in writeStructure() uses all of the atoms to
calculate the VDW energy. As a result atomic overlap between the
probe conformers are counted (presumably because they aren't sensitive
to the constrain statement).
I also get high VDW energies when I use XplorPot("VDW").calcEnergy() to
calculate the VDW energy
How can I calculate the VDW energies for atoms in the proteins in the
complex and not the overlapped mtsl conformers?
Thanks very much!
-Rob
--
Robert Clubb
Professor
Department of Chemistry and Biochemistry
Boyer Hall (Rm 602)
UCLA
611 Charles E. Young Dr. E.
Los Angeles, CA 90095-1570
office: (310)206-2334
Lab: (310)206-3044
Fax: (310)206-4779
Email: rclubb at mbi.ucla.edu
