I have just started using modeller with the help of tutorial example.In
the aligning step when iam aligning 1bdm with TvLDH IAM getting error
only 317 residue out of 318 contain atom of type CA .
That's not an error, it's a warning. It means exactly what it says - one
of your residues doesn't have a CA (C-alpha) atom in it. If your
residues are all supposed to be amino acids, this can be an indication
of a problem. But if you have a ligand in there, most likely it won't
have a CA atom so all is fine.