- This topic has 1 reply, 2 voices, and was last updated 9 years, 6 months ago by Anonymous.
May 12, 2014 at 11:42 am #1888Anonymous
I am using ambiguous constraint file which looks as follows:
AtomPair CB 5 CB 16 BOUNDED 2.500 5.500 0.300 NOE
AtomPair CB 5 CG 16 BOUNDED 2.500 5.500 0.300 NOE
AtomPair CB 5 CD 16 BOUNDED 2.500 5.500 0.300 NOE
AtomPair CG 5 CB 16 BOUNDED 2.500 5.500 0.300 NOE
AtomPair CG 5 CG 16 BOUNDED 2.500 5.500 0.300 NOE
AtomPair CG 5 CD 16 BOUNDED 2.500 5.500 0.300 NOE
AtomPair CB 5 CB 81 BOUNDED 2.500 5.500 0.300 NOE
AtomPair CG 5 CB 81 BOUNDED 2.500 5.500 0.300 NOE
I get following error:
core.io.constraints: read constraints from /exthome1/anusmita/with_constraints_ambiguous_cen/working/test_wth_all/ambig_const/degenerate/ambi_cb_const.cst
[ERROR] Exception caught by JobDistributor for job S_00001Atom CD 16 not found
protocols.jd2.JobDistributor: S_00001 reported failure and will NOT retry
whwreas 16th residue is a Leu and definitely has a CD atom.
Please help me regarding this.
Is there any other format which can be used to mention ambiguous constraints?
May 12, 2014 at 3:25 pm #10045Anonymous
First off, I’ll mention the distinction between pose numbering (sequential starting at 1) and PDB numbering (the number and chain in the PDB file). The constraint file is expecting pose numbering here, so you really do want the “16th residue” (counting from one), rather than the residue which is labeled as number 16 in the input PDB file (if the two are different). Another complication is that if Rosetta skips any residue (e.g. because of zero occupancy of the backbone), the residue which you think is 16th and the one which Rosetta thinks is 16th may be different.
That said, I don’t think the issue is with the constraint file format or residue numbering. Instead, I’m guessing you’re running a protocol which uses a centroid mode stage. In centroid mode, the sidechains are replaced by a single united-atom pseudo atom, so a centorid-mode Leu doesn’t have a CD atom. For centroid mode, you need to base your constraints off of the backbone heavy atoms, rather than sidechain atoms.
Note that you can specify different constraint files for centroid mode and full atom mode. So what you’ll probably want to do is use the above constraint file with “-constraints:cst_fa_file”, and then make a new file (specified with “-constraints:cst_file”) which adjusts/translates the distances and ranges based on sidechain atoms to ones based on the backbone atom positions. It’s okay to be a little bit looser in range here, as you typically will be passing the centroid structure through fullatom refinement, where you’ll use your more exact fullatom constraints.
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