It seems there are some differences with respect to non-standard residues between Modeller4 and Modeller6v2.
I'm working on conotoxin. Some conotoxin sequences include non-standard residues. (such as 1OMC.pdb includes HYP)
When I used Modeller4 before, I modified the template file("HETATM" into "ATOM "), then did alignment and modelling.
The non-standard residues were read as "B".
I'm currently using Modeller6v2. When I did the same things, these residues were read as "G". So the program always
complain "the sequence is different with structure."
Maybe a dirty solution is : modify the template file, delete surplus atoms, change the non-standard residue into
standard residue. But non-standard residues are important for the function of conotoxin.
Is there a better way to deal with non-standard residues?
It seems that "SET HETATM_IO=ON" can not solve this problem.
Thank you very much!
With best regards,
National University of Singapore
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