when i corrected my alignment file as suggested, instead of getting bus
error, now i`m getting segmentation fault. it seems there is still some
problem with the alignment file.
Your alignment is still incorrect; Modeller gives the error:
rdabrk__290E> Number of residues in the alignment and pdb files are
different: 468 30
Your alignment header reads
structureX:1srp:101 : :130 : :srp:Abc de: 1.80: 0.22
i.e. you are telling Modeller that it corresponds to residues 101
through 130 in the PDB file, i.e. 30 residues. But your alignment has
what looks like the whole sequence. Correct your alignment and
everything should work.