Hello again,
This is the end of my log-file:
#################################################### Read the alignment from file : 1ZPA-1A8GA.ali Total number of alignment positions: 99
# Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1A8GA 99 1 1A8GA Comeon 2 1ZPA 99 1 1ZPA Comeon runcmd______> alignment.check()
check_a_343_> >> BEGINNING OF COMMAND openf5__224_> Open 11 OLD SEQUENTIAL .\examples\atom_files\1A8GA.pdb rdpdb___303E> No atoms were read from the specified input PDB file, since the starting residue number and/or chain id in MODEL_SEGMENT (or the alignment file header) was not found; requested starting position: 1A : rdabrk__288W> Protein not accepted: 1 check_a_337E> Structure not read in: 1 ####################################################
and here's my alignment file, I followed what I saw on the link that you sent me.
>P1;1A8GA structureX:1A8GA:1 : :99 : :HIV1 PR: : 1.90: 0.19 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYD QILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF*
>P1;1ZPA sequence:1ZPA:1 : :99 : :HIV1 PR: : 1.90: 0.19 PQITLWKRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYD QILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF*
Could you please let me know what might be the problem?
Thanks, Omid K.