Reply To: Docking an iron atom to a peptide

[Anonymous]

Hi smlewis,

Thanks! This worked perfectly! The rosetta database that I was using didn’t pass the checksum, so I switched to one that did have a correct checksum, and this problem cleared itself up.

Next problem! I ran the AbinitoRelax code again, using modified a FASTA file and the code exited with this error:

ERROR: Conformation: fold_tree nres should match conformation nres. conformation nres: 26 fold_tree nres: 32

I have modified the .tetraL.fa_cst, .cen_cst files, but don’t know what to do with the .residue_pair_jump_cst file, as I’m not too sure what the entries mean.

For your information, the metal binding moiety that I want to use is tetrahedral binding around the metal, with 4 cysteines coordinating the metal atom. These cysteines are at positions 10,11, 19 and 22 in from a primary sequence of 25 aa plus Fe. (26 total residues).

Here is the .residue_pair_jump_cst file as it stands now (unchanged from the original in the metalloprotein_abrelax demo):

BEGIN
jump_def: 5 32 31 31
aa: CYS ZN
cst_atoms: SG CB CA ZN V1 V2
jump_atoms: N CA C ZN V1 V2
disAB: 2.20
angleA: 68.0
angleB: 70.5
dihedralA: -150.0 -120.0 -90.0 -60.0 -30.0 0.0 30.0 60.0 90.0 120.0 150.0 180.0
dihedralAB: -150.0 -120.0 -90.0 -60.0 -30.0 0.0 30.0 60.0 90.0 120.0 150.0 180.0
dihedralB: 120.0
END

Here is the tetraL.fa_cst file:

AtomPair SG 10 V1 26 HARMONIC 0.0 0.2
Angle CB 10 SG 10 ZN 26 HARMONIC 1.95 0.35
AtomPair SG 11 V2 26 HARMONIC 0.0 0.2
Angle CB 11 SG 11 ZN 26 HARMONIC 1.95 0.35
AtomPair SG 19 V1 26 HARMONIC 0.0 0.2
Angle CB 19 SG 19 ZN 26 HARMONIC 1.95 0.35
AtomPair SG 22 V2 26 HARMONIC 0.0 0.2
Angle CB 22 SG 22 ZN 26 HARMONIC 1.95 0.35

And the cen_cst file:

AtomPair CB 10 ZN 26 HARMONIC 3.2 0.2
AtomPair CB 11 ZN 26 HARMONIC 3.2 0.2
AtomPair CB 19 ZN 26 HARMONIC 3.5 0.2
AtomPair CB 22 ZN 26 HARMONIC 3.2 0.2

Thanks! and all the best,

–Buz