I know this error usually happens when I get the names incorrectly. However, in this case, everything is fine and it seems to run for a little while, then it starts writing stuff to my .ali file and give the below error.

readlinef__W> File: alpha_tubulin.pdb, Line: 4611 Modeller will only read the first 80 characters of this line.

readlinef__W> File: alpha_tubulin.pdb, Line: 4612 Modeller will only read the first 80 characters of this line.

readlinef__W> File: alpha_tubulin.pdb, Line: 4613 Modeller will only read the first 80 characters of this line.

readlinef__W> File: alpha_tubulin.pdb, Line: 4614 Modeller will only read the first 80 characters of this line.

readlinef__W> File: alpha_tubulin.pdb, Line: 4615 Modeller will only read the first 80 characters of this line.

readlinef__W> File: alpha_tubulin.pdb, Line: 4616 No more warnings will be printed for truncated lines in this file.

mkapsa__637W> No residue topology library is in memory. Better radii would be used if topology.read() is called first. iup2crm_280W> No topology library in memory or assigning a BLK residue. Default CHARMM atom type assigned: N --> N This message is written only for the first such atom.

Pairwise dynamic programming alignment (ALIGN2D): Residue-residue metric : $(LIB)/as1.sim.mat Diagonal : 100 Overhang : 0 Maximal gap length : 999999 Local alignment : F MATRIX_OFFSET (local aln): 0.0000 FIX_OFFSETS : 0.0 -1.0 -2.0 -3.0 -4.0 N_SUBOPT : 0 SUBOPT_OFFSET : 0.0000 Alignment block : 1 Gap introduction penalty : -100.0000 Gap extension penalty : 0.0000 Gap diagonal penalty : 0.0000 Structure gap penalties : 3.500 3.500 3.500 0.200 4.000 6.500 2.000 0.000 Break-break bonus : 10000.0000 Length of alignment : 441 Score : 258659.2969 read_al_230W> Alignment code alpha_tubulin is present multiple times in the alignment file! Only the first entry will be read. Suggest you remove the duplicate(s) to avoid confusion. read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 1) = alpha_tubulin.pdb Traceback (most recent call last):

File "<ipython-input-12-d935bbc074eb>", line 1, in <module>

runfile('/home/labusr/Desktop/chlamy_paper/denovo_prediction/alpha_tubulin/Modeller/modeller.py', wdir='/home/labusr/Desktop/chlamy_paper/denovo_prediction/alpha_tubulin/Modeller')

File "/home/labusr/anaconda3/lib/python3.5/site-packages/spyderlib/widgets/externalshell/sitecustomize.py", line 714, in runfile execfile(filename, namespace)

File "/home/labusr/anaconda3/lib/python3.5/site-packages/spyderlib/widgets/externalshell/sitecustomize.py", line 89, in execfile exec(compile(f.read(), filename, 'exec'), namespace)

File "/home/labusr/Desktop/chlamy_paper/denovo_prediction/alpha_tubulin/Modeller/modeller.py", line 35, in <module> a.make()

File "/home/labusr/anaconda3/lib/python3.5/site-packages/modeller/automodel/automodel.py", line 112, in make self.homcsr(exit_stage)

File "/home/labusr/anaconda3/lib/python3.5/site-packages/modeller/automodel/automodel.py", line 535, in homcsr aln = self.read_alignment()

File "/home/labusr/anaconda3/lib/python3.5/site-packages/modeller/automodel/automodel.py", line 502, in read_alignment aln.append(file=self.alnfile, align_codes=codes)

File "/home/labusr/anaconda3/lib/python3.5/site-packages/modeller/alignment.py", line 80, in append allow_alternates)

ModellerError: read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 1) = alpha_tubulin.pdb