Reply To: loop model error

[Anonymous]

Thank you very much. The seeds works now.But it still cannot generate models. it is said:

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log

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core.io.pdb.file_data: [ WARNING ] can’t find atom for res 1 atom OG (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 4 atom CD1 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 4 atom CD2 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 4 atom CE1 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 4 atom CE2 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 4 atom CG (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 4 atom CZ (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 4 atom OH (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 5 atom CD1 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 5 atom CD2 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 5 atom CG (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 6 atom CD1 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 6 atom CD2 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 6 atom CE1 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 6 atom CE2 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 6 atom CG (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 6 atom CZ (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 7 atom CD1 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 7 atom CD2 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 7 atom CG (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 8 atom CG (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 8 atom OD1 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 8 atom OD2 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 9 atom CD (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 9 atom CG1 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 9 atom CG2 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 10 atom CD (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 10 atom CG1 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 10 atom CG2 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 11 atom CG2 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 11 atom OG1 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 12 atom CD1 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 12 atom CD2 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 12 atom CE1 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 12 atom CE2 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 12 atom CG (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 12 atom CZ (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 12 atom OH (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 13 atom CD1 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 13 atom CD2 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 13 atom CG (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 14 atom CG1 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 14 atom CG2 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 15 atom CD1 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 15 atom CD2 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 15 atom CE1 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 15 atom CE2 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 15 atom CG (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 15 atom CZ (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 17 atom CG1 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 17 atom CG2 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 18 atom CG2 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 18 atom OG1 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 19 atom CD1 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 19 atom CD2 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 19 atom CE1 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 19 atom CE2 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 19 atom CG (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 19 atom CZ (trying to set temp)
core.io.pdb.file_data: [ WARNING ]
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protocol.loops.LoopMover: Setting extended torsions: LOOP 64 75 73 0 1
protocol.loops.LoopMover: Building Loop: LOOP 64 75 73 0 1
protocol.loops.LoopMover: Building Loop attempt: 0
protocol.loops.LoopMover: perturb_one_loop_with_KIC: 64 12
protocol.loops.LoopMover: remodel init temp: 2
protocol.loops.LoopMover: remodel final temp: 1
protocol.loops.LoopMover: kinematic initial perturb with start_res: 64 middle res: 69 end_res: 75
protocol.loops.LoopMover: loop rmsd before initial kinematic perturbation:0
protocol.loops.LoopMover: Attempting loop building: 0 …
protocol.loops.LoopMover: Attempting loop building: 1 …
protocol.loops.LoopMover: Attempting loop building: 2 …
protocol.loops.LoopMover: Attempting loop building: 3 …
protocol.loops.LoopMover: Attempting loop building: 4 …
protocol.loops.LoopMover: Attempting loop building: 5 …
protocol.loops.LoopMover: Attempting loop building: 6 …
protocol.loops.LoopMover: Attempting loop building: 7 …
protocol.loops.LoopMover: Attempting loop building: 8 …
protocol.loops.LoopMover: Attempting loop building: 9 …
protocol.loops.LoopMover: Attempting loop building: 10 …
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can’t find atom for res 20 atom CG1 (trying to set temp)

protocol.loops.LoopMover: [WARNING] Failed to build loop with kinematic Mover during initial kinematic perturbation after 100 trials: LOOP 64 75 64 0 1
protocol.loops.LoopMover: Unable to build this loop – a critical error occured. Moving on ..
protocol.loops.LoopMover: Loopstat: 64 75 64 75 12 time 6.5 1 time 6.5 1e+07 ext
protocols.looprelax: Structure failed initial kinematic closure. Skipping…
protocols::checkpoint: Deleting checkpoints of Remodel
protocols::checkpoint: Deleting checkpoints of Loopbuild