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