[modeller_usage] "Structure not read in" error

["Omid Khalouei" <omid9dr18@hotmail.com>]

Hello,

I am just starting to use Modeller. Even though I have a major in computer 
science, have used many bioinformatics tools, and am familiar with Python, I 
haven't been able to figure out how to run this program. To be honest I 
don't find it that user-friendly!
Basically I'm not sure in which folder I have to put my alignment and PDB 
coordinate files. This is the alignment file that I have created but am not 
sure if it meets the specifications (they both refer to HIV-1 protease, 
residues 1 to 99 of chain A);
   P1;1A8GA

structureX:1A8GA:1:A 99:A:.:.:.:.
PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYD
QILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF*


   P1;1ZPA

sequence:1ZPA:1:A 99:A:.:.:.:.
PQITLWKRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYD
QILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF*

The error message that I'm getting is "Structure not read in:    1" and it's 
raised from the Modeller8v1\modlib\modeller\util\top.py file.
I would appreciate your help on this.
Omid K.