10 Nov
1999
10 Nov
'99
9:06 a.m.
I generated several loop conformations using the 'loop' routine. The top file is similar to example 3 of the manual, with the addition of gemetrical constraints on the end of loops.
I am refining 20 a.a. out of a 27-loop segment.
The refined loop conformations still have residues located in unfavorable regions of the phi/psi plot, i.e. phi> 0 (non Gly, or Asn). Typically, there are 1-4 residues in these regions. Only 2% of my conformations have all residues with phi<0. Are such occurrencies typical of the refinement procedure? If not, how can I prevent this for happening?
Thanks Germana
Germana Paterlini Dept. of Medicinal Chemistry Minneapolis, MN 55455 germana1@vwl.medc.umn.edu