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Homology modeling

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Homology modeling


Is there good documentation or a tutorial on how to use Rosetta 3.0 to construct a homology model based on a user-input template?

Documentation is not clear (or is absent).

Any help is most welcomed. I am able to generate a backbone model, but unable to generate a fullatom model.

thanks, Mike

Mon, 2009-08-17 13:04

The error I am getting when running the following:

-database /usr/local/rosetta3.0/rosetta3_database
-nstruct 2
-loops::input_pdb template.pdb
-loops::loop_file loops.file
-loops::frag_sizes 9 3
-loops::frag_files aaquery09_05.200_v1_3 aaquery03_05.200_v1_3


"ERROR: Could not find disulfide partner for residue"

Mon, 2009-08-17 13:23

Do you have disulfides in your protein?

As of 3.0, the "detect_disulfides" flag defaults to true, you can try turning this to false, especially if you do not have disulfides.

There is a flag "fix_disulf" which lets you specify where you know the disulfides are - I've never used it and have no idea if it's compatible with loop modeling.

Tue, 2009-08-18 10:49