Alignment Rules:

• Make sure that there is no special  characters, like space coma or non alphanumeric character in the template/target. 
• Gaps should be indicated by "-" and not by "."
• In case of disulfide bond in the template, replace  CYS (C) residue in the target by small letter "c".
• Only 20 capital alphabets and one small alphabet for Cys, c is accepted.
• Sometime selenomethionine will be indicated by  "X". Edit this to "M" and edit the template pdb file accordingly.
• Sometime in sequence alignment there are unknown residues are marked with "X". One should edit it back to the original residue if any in PDB file.
• If one wants to use multiple templates or small fragments then appropriate  alignments containing those regions should be given as an alignment  (starting number of the target residue contained in these files should be mentioned separately).  All alignment files must follow the alignment rules.
• Template PDB files can be obtained from RCSB (http://www.rcsb.org).  Almost in all cases to have consistency while modeling it is recommended to spend time to look into the header files of the PDB. In some cases it may be required to edit the file.
• Read carefully the SS Bonds information from PDB file. If you have any matching CYS residues in the template and the target, then most probably the target may also have similar SS bonds.
• Make sure that the amino acid residues in the target PDB file and the alignment must match exactly, otherwise it will crash the program before run.
  
• Target PDB file should end with TER followed by END and the PDB file must have extension "*.pdb"