Ben,

thanks for suggestions!

The problem was in the charm-like naming of the Histidine residues in the input.pdb ( so its produce mismatch). Does it possible to make some aliases for HIS HSP HSE HSD (to His in sequence entry) as well as other titrable residues ?


James

2013/6/24 Modeller Caretaker <modeller-care@salilab.org>
On 6/24/13 1:50 AM, James Starlight wrote:
_modeller.SequenceMismatchError: get_ran_648E> Alignment sequence not
found in PDB file:        1  ./input.pdb (You didn't specify the
starting and ending residue numbers and chain IDs in the alignment, so
Modeller tried to guess these from the PDB file.) Suggestion: put in the
residue numbers and chain IDs (see the manual) and run again for more
detailed diagnostics. You could also try running with
allow_alternates=True to accept alternate one-letter code matches (e.g.
B to N, Z to Q).


How I could fix it ?

Did you try doing what the error suggests? You didn't include input.pdb, so I can't be sure, but it's quite possible that it doesn't have a chain with no ID (as you specified in your alignment) but that it has an "A" chain.

        Ben Webb, Modeller Caretaker
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