fixbb and ncaa’s

[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 B48

and 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.txt

now when I run it, I get this:
core.pack.task.ResfileReader: On line 3 command ‘A20’is not recognized

Do I need to do anything else to have the ncaa’s available for fixbb ?

Thanks

Jarek

[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

[Anonymous]

is there a way to include all ncaa’s and caa’s at once?

[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?

[Anonymous]

There is no way to include all available NCAAs simultaneously. ALLAA allows all the canonical types.

[Author]

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