Focus on the statement with ALIGN_CODES, as it is inclusive of the PDB_ID and the PDB_CHAIN used in the alignment file. So it could probably be '2AHNA' or '2AHNB'.

Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA

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Message: 2 Date: Mon, 9 Apr 2012 17:21:12 +0530 From: Sumedha Roy sumedharoy@gmail.com To: modeller usage modeller_usage@salilab.org Subject: [modeller_usage] Error in ALIGN_CODES(i) Message-ID: CABFmE0dNMawUwZgsh07bsRd43+-O3Yrzq6VhfkSQJOTjp=NECA@mail.gmail.com Content-Type: text/plain; charset="iso-8859-1"

Hello all,

When I try to model my protein-DNA complex, I get the error: _modeller.ModellerError: read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 2) = 2AHN

But I see no mistake either in the alignment or the format. I've attached both the ALI file and model-ligand.py. Please help!!!