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Re: [modeller_usage] error in using a simulated structure as template.

On 4/28/11 7:52 AM, Bala subramanian wrote:

I am a newbie to modeller. I have the structure of a protein obtained
from MD simulation (total 339 residues). I have another sequences of
unknown structure ( total 345 residues). I want to model the structure
of the later by using the simulated structure as template.

I first aligned the two sequences with clustwal  and made the .ali file
(pasted below) . The modeller script i used is attached. Kindly write me
what is going wrong ?
Like the error message says, the sequence in your alignment file does not match that in the PDB file. They must match exactly. The Modeller log file will tell you where the mismatch is, so that you can correct your alignment file. 

	Ben Webb, Modeller Caretaker
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