I received an error while running PEP-FOLD 3.5. The error output is attached below. But it appears be looking for a file cluster.txt that it can’t find. I don’t believe this is an input option. Could you please advise on how to correct this issue?
Shake mask : 000000000000000 (aaMskSeq: PKVDIWSLGIMAIEMIEG)
CppBuilder --objective carmsd --action pepbuild --generator fbt --3D_dmn --iTemplate SKIP.shake_pdb --iSeq SKIP.seq --label SKIP-rebuild --rndFrom 200 --heapSze 600 --mcSteps 10000 --nc 8 --nSim 8 --seed -1
PEP-FOLD 3 Initial start: True
PEPFOLD v1.0
s4TrjFile: None
verbose: True
reference: None
demo: None
runsFrom: 1
simFromTo: None
seqFile: iSeq.data
model2016: False
doPostTT: True
sortbysize: False
seed: 522814
maxSimSze: 50
do3D: True
autoFromTo: False
sge: False
CSFile: None
PPPOnly: False
maxSeqSze: 50
sgemap: False
generator: ts5
script: False
shakePos: 14
label: SKIP
demo_complex: None
neighbours: None
combined: False
model2012: False
userTrj: None
refZones: None
pepfold1: False
modelOffset: 0
SSBonds: None
doClusters: True
medium: False
doPPP: True
receptor_patch: residues_list.data
model2006: False
input_peptide_model: Pak1_433-460-Renumbered_1-18.pdb
shortcombined: False
shakeMaskFile: SKIP.shakemask
runGreedy: True
nCores: 8
doMQA: True
runClusters: True
extBias: False
CS: False
bestTrj: SKIP-rebuild-00007_bestene1-mc.trj
runPPP: True
CSTabFile: None
simType: PEPMODEL
runPostTreatment: True
doHTMLFormatting: True
clusteringOnly: False
trjCnstr: SKIP-rebuild.cnstr.trj
mcSteps: 30000
sgePostTreat: False
sortKey: sOPEP
postTreatmentOnly: False
demo_shake: None
input_shake_mask: iRefMask.data
greedyOnly: False
doAddEnergy: False
debug: False
receptor: INPP5K_SKICH_Domain_Renumber_1-104.pdb
runClustering: True
ppfld_centroids: 10
SVM2012: False
nRuns: 100
PyPPP3Exec -s iSeq.data -l SKIP -v --2012
CppBuilder_service --objective sopep --action pepbuild --generator ts --iPrf SKIP.svmi8.27.prob --iSeq SKIP.seq --label SKIP --rndFrom 100 --heapSze 300 --mcSteps 30000 --nc 8 --nSim 100 --prfFilter none --ts_sze 5 --seed 522814 --iTrjCnstr SKIP-rebuild.cnstr.trj --iReceptor SKIP.receptor_pdb --iOriginCrdFile SKIP.start_crds --chPiv 1000 --outModelOffset 0
CppBuilder_service --objective sopep --action pepbuild --generator ts --iPrf SKIP.svmi8.27.prob --iSeq SKIP.seq --label SKIP --rndFrom 100 --heapSze 300 --mcSteps 30000 --nc 8 --nSim 100 --prfFilter none --ts_sze 5 --seed 522814 --iTrjCnstr SKIP-rebuild.cnstr.trj --iReceptor SKIP.receptor_pdb --iOriginCrdFile SKIP.start_crds --chPiv 1000 --outModelOffset 100 --extBias 0.100000
POSTTTExec --mask “ene1-mc.pdb" --oscar --pattern "-ID_bestene1-mc.pdb” --parallelposttreatment --noSuperpose --padding 5 --silent -v
Traceback (most recent call last):
File “/service/env/PEPFOLD3.5/PEPFOLD3.py”, line 1323, in
main(sys.argv)
File “/service/env/PEPFOLD3.5/PEPFOLD3.py”, line 1315, in main
job.runPepFold(verbose = True)
File “/service/env/PEPFOLD3.5/PEPFOLD3.py”, line 1216, in runPepFold
self.runClustersTools()
File “/service/env/PEPFOLD3.5/PEPFOLD3.py”, line 984, in runClustersTools
f = open(“clusters.txt”)
IOError: [Errno 2] No such file or directory: ‘clusters.txt’
Session information:
- id: R24057906362057
- email: None
- activated?: True
- authenticated?: False
Job information:
- id: RPBS Web Portal
- date: Sun, 19 Jun 2022 21:33:49 +0000
- status: finished
- user error in parameter: None
- user error message: None