Anagha Joshi wrote: > when I try to run the basic model tutorial at modeller site > I run align2d.top > I get warning > mkapsa__293W> No TOPOLOGY_LIB is in memory. Use READ_TOPOLOGY to read one. > iup2crm_280W> No TOPOLOGY_LIB in memory or assigning a BLK residue. > Default CHARMM atom type assigned: C --> CT2 > This message is written only for the first such atom. > fndatmi_285W> Number of residues <> number of atoms; atom code: 668 > 66 > 6 CA > fndatmi_285W> Number of residues <> number of atoms; atom code: 668 > 66 > 6 CA > I > don,t > understand what this warning is.

It is only a warning, and can be ignored in this case. If you are going to build a comparative model, then Modeller needs to know that a 'CT2' atom is a carbon, so that it can match it against similar carbon atoms in the templates, and use molecular mechanics parameters defined for a CT2 atom. It gets this information from the topology and parameter files. However, for the case of alignment, this is not needed.

Ben Webb, Modeller Caretaker -- modeller-care@salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage