Reply To: Loop Modeling

[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