Reply To: Ab Initio Modelling of Protein with Small-Molecule Cofactor

[Anonymous]

Yes, scombs, I added FAD in brackets as the last letters in my fasta sequence file.

The flag seemed okay. What really did the trick was rmoretti’s suggestion not only to feed in a full atom parameter file but also to generate a centroid one.

So I am beyond that first problems now. What I am now getting relates somehow to the declaration of constraints.

The error message is the following:

[..some text..]
core.scoring.constraints: Constraint choice: ./prot.cen_cst
core.io.constraints: read constraints from ./prot.cen_cst
core.io.constraints: read constraints section –NO_SECTION—
core.io.constraints: no section header [ xxx ] found, try reading line-based format… DON’T MIX
core.io.constraints: read constraints from ./prot.cen_cst
core.io.constraints: ignored constraint (no such atom in pose!)CB O7 41 129
core.io.constraints: ERROR: reading of AtomPair failed.
core.io.constraints: ERROR: reading constraints from file./prot.cen_cst
[..some text.. without errors]
protocols.abinitio:
===================================================================
Stage 1
Folding with score0 for max of 2000
segmentation fault

So Rosetta actually tries to start that calculation but fails later. I tried running everything without the cofactor, the constraints etc. and that works. The problem seems to lie with the constraints. I kept to the constraints definition as it can be found in the abinitio_metalloprot_folding demo.

Here is, how I did it:
AtomPair CB 41 O7 129 HARMONIC 5.9 0.5
AtomPair CB 46 O5 129 HARMONIC 5.4 1.0
AtomPair CB 74 O8 129 HARMONIC 5.0 0.5
AtomPair CB 84 O9 129 HARMONIC 5.0 0.5
AtomPair CB 103 O9 129 HARMONIC 5.6 1.0

“129” is the pseudo-sequence number of FAD since I’ve got 128 residues in that protein chain. O5, O7, O8 and O9 are the oxygen atoms in nomenclature as found in the params file (would be O2′, O4′, O2, O4) otherwise.