Reply To: Loop Modeling

[JianyiYang]

I get the same errors when I run the loop modelling demo that came with the Rosetta3.0 package. Has anyone gotten this demo to run w/o getting warning messages? Is the demo incorrect? It looks the demo is reading it in as a full atom, despite only backbone being provided. However, I still get errors when I remove the full atom from the flags file.

Here are the errors from the demo.
core.conformation.Conformation: [ WARNING ] missing heavyatom: CEN on residue MET_p:NtermProteinFull 1
core.conformation.Conformation: [ WARNING ] missing heavyatom: CEN on residue LYS 2
core.conformation.Conformation: [ WARNING ] missing heavyatom: CEN on residue ILE 3
core.conformation.Conformation: [ WARNING ] missing heavyatom: CEN on residue VAL 4
core.conformation.Conformation: [ WARNING ] missing heavyatom: CEN on residue TYR 5
core.conformation.Conformation: [ WARNING ] missing heavyatom: CEN on residue TRP 6
core.conformation.Conformation: [ WARNING ] missing heavyatom: CEN on residue SER 7
core.conformation.Conformation: [ WARNING ] missing heavyatom: CEN on residue GLY 8
core.conformation.Conformation: [ WARNING ] missing heavyatom: CEN on residue THR 9
core.conformation.Conformation: [ WARNING ] missing heavyatom: CEN on residue GLY 10
core.conformation.Conformation: [ WARNING ] missing heavyatom: CEN on residue ASN 11
core.conformation.Conformation: [ WARNING ] missing heavyatom: CEN on residue THR 12
core.conformation.Conformation: [ WARNING ] missing heavyatom: CEN on residue GLU 13
core.conformation.Conformation: [ WARNING ] missing heavyatom: CEN on residue LYS 14
core.conformation.Conformation: [ WARNING ] missing heavyatom: CEN on residue MET 15
core.conformation.Conformation: [ WARNING ] missing heavyatom: CEN on residue ALA 16
core.conformation.Conformation: [ WARNING ] missing heavyatom: CEN on residue GLU 17
core.conformation.Conformation: [ WARNING ] missing heavyatom: CEN on residue LEU 18

---

core.pack.pack_missing_sidechains: packing residue number 1 because of missing atom number 6 atom name CG
core.pack.pack_missing_sidechains: packing residue number 2 because of missing atom number 6 atom name CG
core.pack.pack_missing_sidechains: packing residue number 3 because of missing atom number 6 atom name CG1
core.pack.pack_missing_sidechains: packing residue number 4 because of missing atom number 6 atom name CG1
core.pack.pack_missing_sidechains: packing residue number 5 because of missing atom number 6 atom name CG
core.pack.pack_missing_sidechains: packing residue number 6 because of missing atom number 6 atom name CG
core.pack.pack_missing_sidechains: packing residue number 7 because of missing atom number 6 atom name OG
core.pack.pack_missing_sidechains: packing residue number 9 because of missing atom number 6 atom name OG1
core.pack.pack_missing_sidechains: packing residue number 11 because of missing atom number 6 atom name CG
core.pack.pack_missing_sidechains: packing residue number 12 because of missing atom number 6 atom name OG1
core.pack.pack_missing_sidechains: packing residue number 13 because of missing atom number 6 atom name CG
core.pack.pack_missing_sidechains: packing residue number 14 because of missing atom number 6 atom name CG

>You’ve got a centroid/full atom mismatch.

>It looks like your relax result is fullatom, but your loop modeling is in centroid mode. You >probably need to pass a flag to loop modeling to make it run in full atom mode – hopefully the >loop modeling documentation shows which one. (It’s pretty dumb that you need a second flag for >this, I know…)