Member Site › Forums › Rosetta 3 › Rosetta 3 – Applications › fixbb and ncaa’s
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Anonymous.
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November 8, 2012 at 12:55 pm #1456
Anonymous
I am trying to use the fixbb application with non-canonical amionoacids.
I have prepared a test res file:NATRO
start
23 B EMPTY A20 B47 B48and use the -score:weights mm-std flag
I have also de-commented the l-ncaa aminoacids in the chemical/residue_type_sets /fa_standard/residue_types.txtnow when I run it, I get this:
core.pack.task.ResfileReader: On line 3 command ‘A20’is not recognizedDo I need to do anything else to have the ncaa’s available for fixbb ?
Thanks
Jarek
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November 8, 2012 at 2:47 pm #8054
Anonymous
Yes, you forgot the NC command, that signals the resfile reader that the following residue names are noncanonicals.
You need your line to look like this:
23 B EMPTY NC A20 NC B47 NC B48 -
November 8, 2012 at 3:45 pm #8058
Anonymous
is there a way to include all ncaa’s and caa’s at once?
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December 21, 2017 at 6:13 pm #13967
Anonymous
First Issue:
I have been trying to use fixbb to modify and select new sequences on cyclized and linear NCAA chains.
On cyclized molecules (generated in cyc_pep_pred with sequence: (N-methylated Gly)*6 ) the fixbb code reports success with resfile (NATRO; start; 1 A EMPTY NC 601), but the actual sequence and structure are not changed.
I know that the structures I am working with should allow these new non-canonical residues to be added from MutateResidue runs that did not perturb the orientation of the branching point.
For linear NCAA chains I have worked on a hybrid alanine:sarcosine(peptoid:201) chain ([201:A:201:A:201:A:201:A]).
The resfile can modify the canonical amino acid A into peptoid:601, but it CANNOT modify the ‘201’ to ‘601’.
The code complaint is in the AtomICoor.cc:200: “unrecognized stub atom id type!”
Can fixbb not operate on non-canonical residues that are already in the input structure?
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November 8, 2012 at 3:48 pm #8059
Anonymous
There is no way to include all available NCAAs simultaneously. ALLAA allows all the canonical types.
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