Hi Hussain, I think you need to edit your input file and increase the max number of chain and the max number of tree . I had this problem several times especially if the structure is big or the chain(s) is(are) fragmented. The default values in CNS usually work but you can increase them and it should go through.
HTH -- Pascal F. Egea, PhD Assistant Professor UCLA, David Geffen School of Medicine Department of Biological Chemistry 314 Biomedical Sciences Research Building office (310)-983-3515 lab (310)-983-3516 email pe...@mednet.ucla.edu