Loop Modeling

[JianyiYang]

Hi,

I am trying to take the output from the relax module and put it into the loop modelling module. I’m getting the following errors:

core.io.pdb.file_data: [ WARNING ] discarding 5 atoms at position 1 in file CeQ03.B99990001_0001.pdb. Best match rsd_type: GLY_p:NtermProteinFull
core.io.pdb.file_data: [ WARNING ] discarding 9 atoms at position 2 in file CeQ03.B99990001_0001.pdb. Best match rsd_type: GLU
core.io.pdb.file_data: [ WARNING ] discarding 18 atoms at position 3 in file CeQ03.B99990001_0001.pdb. Best match rsd_type: TRP
core.io.pdb.file_data: [ WARNING ] discarding 18 atoms at position 4 in file CeQ03.B99990001_0001.pdb. Best match rsd_type: ARG
core.io.pdb.file_data: [ WARNING ] discarding 4 atoms at position 5 in file CeQ03.B99990001_0001.pdb. Best match rsd_type: ALA
core.io.pdb.file_data: [ WARNING ] discarding 18 atoms at position 6 in file CeQ03.B99990001_0001.pdb. Best match rsd_type: ARG
core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 7 in file CeQ03.B99990001_0001.pdb. Best match rsd_type: GLY

##############

ore.conformation.Conformation: [ WARNING ] missing heavyatom: CEN on residue GLY_p:NtermProteinFull 1
core.conformation.Conformation: [ WARNING ] missing heavyatom: CEN on residue GLU 2
core.conformation.Conformation: [ WARNING ] missing heavyatom: CEN on residue TRP 3
core.conformation.Conformation: [ WARNING ] missing heavyatom: CEN on residue ARG 4
core.conformation.Conformation: [ WARNING ] missing heavyatom: CEN on residue ALA 5
core.conformation.Conformation: [ WARNING ] missing heavyatom: CEN on residue ARG 6
core.conformation.Conformation: [ WARNING ] missing heavyatom: CEN on residue GLY 7
core.conformation.Conformation: [ WARNING ] missing heavyatom: CEN on residue ARG 8
core.conformation.Conformation: [ WARNING ] missing heavyatom: CEN on residue PRO 9
core.conformation.Conformation: [ WARNING ] missing heavyatom: CEN on residue ARG 10

###############

core.io.pdb.file_data: WARNING can’t find atom for res 1 atom 1H (trying to set temp)
core.io.pdb.file_data: WARNING can’t find atom for res 1 atom 1HA (trying to set temp)
core.io.pdb.file_data: WARNING can’t find atom for res 1 atom 2H (trying to set temp)
core.io.pdb.file_data: WARNING can’t find atom for res 1 atom 2HA (trying to set temp)
core.io.pdb.file_data: WARNING can’t find atom for res 1 atom 3H (trying to set temp)
core.io.pdb.file_data: WARNING can’t find atom for res 2 atom CD (trying to set temp)
core.io.pdb.file_data: WARNING can’t find atom for res 2 atom CG (trying to set temp)
core.io.pdb.file_data: WARNING can’t find atom for res 2 atom HA (trying to set temp)
core.io.pdb.file_data: WARNING can’t find atom for res 2 atom OE1 (trying to set temp)
core.io.pdb.file_data: WARNING can’t find atom for res 2 atom OE2 (trying to set temp)
core.io.pdb.file_data: WARNING can’t find atom for res 2 atom 1HB (trying to set temp)
core.io.pdb.file_data: WARNING can’t find atom for res 2 atom 1HG (trying to set temp)
core.io.pdb.file_data: WARNING can’t find atom for res 2 atom 2HB (trying to set temp)

I did not get any errors while running the relax mode, so I don’t think it is a formatting problem. Any advice would be appreciated!

Thanks!
Christy

[Anonymous]

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…)

[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…)

[JianyiYang]

Thanks for your help. I figured it out. I needed -loops:fa_input

It still doesn’t explain why the demo won’t work, but my case does work now.

> Hi,
>
> I am trying to take the output from the relax module and put it into the loop modelling module. I’m getting the following errors:
>
>
> core.io.pdb.file_data: [ WARNING ] discarding 5 atoms at position 1 in file CeQ03.B99990001_0001.pdb. Best match rsd_type: GLY_p:NtermProteinFull
> core.io.pdb.file_data: [ WARNING ] discarding 9 atoms at position 2 in file CeQ03.B99990001_0001.pdb. Best match rsd_type: GLU
> core.io.pdb.file_data: [ WARNING ] discarding 18 atoms at position 3 in file CeQ03.B99990001_0001.pdb. Best match rsd_type: TRP
> core.io.pdb.file_data: [ WARNING ] discarding 18 atoms at position 4 in file CeQ03.B99990001_0001.pdb. Best match rsd_type: ARG
> core.io.pdb.file_data: [ WARNING ] discarding 4 atoms at position 5 in file CeQ03.B99990001_0001.pdb. Best match rsd_type: ALA
> core.io.pdb.file_data: [ WARNING ] discarding 18 atoms at position 6 in file CeQ03.B99990001_0001.pdb. Best match rsd_type: ARG
> core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 7 in file CeQ03.B99990001_0001.pdb. Best match rsd_type: GLY
>
> ##############
>
> ore.conformation.Conformation: [ WARNING ] missing heavyatom: CEN on residue GLY_p:NtermProteinFull 1
> core.conformation.Conformation: [ WARNING ] missing heavyatom: CEN on residue GLU 2
> core.conformation.Conformation: [ WARNING ] missing heavyatom: CEN on residue TRP 3
> core.conformation.Conformation: [ WARNING ] missing heavyatom: CEN on residue ARG 4
> core.conformation.Conformation: [ WARNING ] missing heavyatom: CEN on residue ALA 5
> core.conformation.Conformation: [ WARNING ] missing heavyatom: CEN on residue ARG 6
> core.conformation.Conformation: [ WARNING ] missing heavyatom: CEN on residue GLY 7
> core.conformation.Conformation: [ WARNING ] missing heavyatom: CEN on residue ARG 8
> core.conformation.Conformation: [ WARNING ] missing heavyatom: CEN on residue PRO 9
> core.conformation.Conformation: [ WARNING ] missing heavyatom: CEN on residue ARG 10
>
> ###############
>
> core.io.pdb.file_data: WARNING can’t find atom for res 1 atom 1H (trying to set temp)
> core.io.pdb.file_data: WARNING can’t find atom for res 1 atom 1HA (trying to set temp)
> core.io.pdb.file_data: WARNING can’t find atom for res 1 atom 2H (trying to set temp)
> core.io.pdb.file_data: WARNING can’t find atom for res 1 atom 2HA (trying to set temp)
> core.io.pdb.file_data: WARNING can’t find atom for res 1 atom 3H (trying to set temp)
> core.io.pdb.file_data: WARNING can’t find atom for res 2 atom CD (trying to set temp)
> core.io.pdb.file_data: WARNING can’t find atom for res 2 atom CG (trying to set temp)
> core.io.pdb.file_data: WARNING can’t find atom for res 2 atom HA (trying to set temp)
> core.io.pdb.file_data: WARNING can’t find atom for res 2 atom OE1 (trying to set temp)
> core.io.pdb.file_data: WARNING can’t find atom for res 2 atom OE2 (trying to set temp)
> core.io.pdb.file_data: WARNING can’t find atom for res 2 atom 1HB (trying to set temp)
> core.io.pdb.file_data: WARNING can’t find atom for res 2 atom 1HG (trying to set temp)
> core.io.pdb.file_data: WARNING can’t find atom for res 2 atom 2HB (trying to set temp)
>
> I did not get any errors while running the relax mode, so I don’t think it is a formatting problem. Any advice would be appreciated!
>
> Thanks!
> Christy

[Author]

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