On 05/10/2013 03:13 AM, Priya Chaudhary wrote: > I have to use a template, whose PDB ID is 1APS. It is *NMR Model *with > four models. > > I have to use only *first model of this NMR* structure.
This is fine - Modeller will only read the first model from NMR structures.
> For this template, I have *50 Query sequences* in 50 separate ".fasta > files" in PIR FORMAT.
Are they FASTA files or PIR files? You need PIR files for modeling.
> *Description of PIR Format of Query sequences:* > > *First line: *>1APS_1; Mutant_Y15M > > *Second Line:* I think this line is optional - I HAVE OMITTED THIS LINE. > My second line is PROTEIN SEQUENCE in Capital letters ending with " * ".
What you describe is not a valid PIR file. You can find a description of the file format at http://salilab.org/modeller/9.11/manual/node476.html
Ben Webb, Modeller Caretaker