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
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