I suggest you explicitly define the heterocompound as a rigid body for torsion dynamics. There are sometimes situations involving closed ring systems that cause this topology generation error.
Axel Brunger On Mar 20, 2010, at 3:46 AM, Suman Tapryal wrote: > Hi all, > > I am trying to calculate composite omit map using CNS. My structure has a > bound molecule of tris. I have generated CNS topology and parameter files > using PRODRG server. The files seem to work fine when I am doing > minimizations and other refinement operations. However, I am getting the > following errors while calculating composite omit map: > > ERROR: There are no suitable base groups. > This problem can be caused by isolated > bonding networks with undefined or weak > dihedral force constants. > The atoms that cannot be placed in a tree > are listed below: > %atoms "T "-1 -TRS -O1 > %atoms "T "-1 -TRS -C1 > %atoms "T "-1 -TRS -C > %atoms "T "-1 -TRS -N > %atoms "T "-1 -TRS -C3 > %atoms "T "-1 -TRS -O3 > %atoms "T "-1 -TRS -C2 > %atoms "T "-1 -TRS -O2 > %TORSION:TOPOLOGY error encountered: Fatal Topology Error > (CNS is in mode: SET ABORT=NORMal END) > > Am I missing out something? > > Regards > > Suman Axel T. Brunger Investigator, Howard Hughes Medical Institute Professor of Molecular and Cellular Physiology Stanford University Web: http://atbweb.stanford.edu Email: brun...@stanford.edu Phone: +1 650-736-1031 Fax: +1 650-745-1463
