Hello Ram,
The problem could be becoz of not converting your *.pdb file into *.ent extension . And also your PDB coordinate file not starting with theh residue number 1 (since in some cases PDB coordinates starts with residue number other that 1) and also make it sure if you deal with single segment of PDB ,remove chain ID from your coordinate data.
Hope it works , For more clarification send me your TOP and Alignment file, I try to fix your problem
Good Luck,
B.Nataraj