I am trying to run the Create Polymer Network Pipeline Pilot protocol using DGEBA and 4,4' DDS as the epoxide and the linker. I have defined the labels R1 and R2 as the reactant sites for DGEBA and 4,4' DDS respectively. I have also altered the Create Polymer Network Protocol as suggested earlier to turn Restrain Rings in the Create Amorphous Cell to True. With these settings, I can sometimes successfully crosslink a structure, but other times the system fails with an error. I have included the Summary.html showing the input as well as the Error.txt file below for reference. Any ideas as to what might be going on? Note that the error happens (or not) regardless of the loading. Note I have also included stick figures of the precursors attached below the text.
I would love to be able to see the code that gives rise to the error (main::RingOpening(Cfx::COM=HASH(0xd12dcf8), Cfx::COM=HASH(0x7756560)) called at (eval 10) line 32), but I don't know how to access the code within Pipeline Pilot. Any suggestions as to what to try to improve reproducibility?
Protocol failed: | Error executing parallel subprotocol on crater.a04.aist.go.jp: 'Unable to find bond to delete |
Parameters
Base Resin | |
Base Resin Source | DGEBA.xsd |
Base Resin Loading | 5 |
Curing Agent | |
Curing Agent Source | 4,4'DDS.xsd |
Curing Agent Loading | 2 |
Solvent | |
Solvent Source | |
Solvent Loading | |
Species | R1 R2 secondary amine |
Reactions | |
Reaction 1 | |
Reaction 1 Reactant1 | R1 |
Reaction 1 Reactant2 | R2 |
Reaction 1 Product1 | X |
Reaction 1 Product2 | secondary amine |
Reaction 1 Probability | 1 |
Reaction 1 Reaction Type | Ring Opening |
Reaction 2 | |
Reaction 2 Reactant1 | secondary amine |
Reaction 2 Reactant2 | secondary amine |
Reaction 2 Product1 | X |
Reaction 2 Product2 | X |
Reaction 2 Probability | 0.5 |
Reaction 2 Reaction Type | Ring Opening |
Reaction Cycle | |
Reaction Cycle Number of Steps (Restrained) | 10000 |
Reaction Cycle Number of Steps (NVT) | 5000 |
Reaction Cycle Number of Steps (NPT) | 5000 |
Reaction Cycle Maximum | 25 |
Conversion | |
Conversion Species | R1 |
Conversion Maximum | 0.95 |
Reaction Radius | |
Reaction Radius Initial | 3 |
Reaction Radius Step | 1 |
Reaction Radius Maximum | 8 |
Preparation | |
Configurations | 1 |
Initial Density | 0.8 |
Preparation Number of Steps (NVT) | 10000 |
Preparation Number of Steps (NPT) | 10000 |
Temperature | 298 |
Pressure | 0.000101325 |
Energy | |
Forcefield | COMPASSII |
Calculate Forcefield Types | True |
Calculate Bond Order | True |
Custom Forcefield File | |
Charges | Forcefield Assigned |
Initial Charge | Formal |
Maximum Charge Iterations | 50 |
Convergence Limit | 5.0e-4 |
Parameter Set | QEq_charged1.1.chg |
Summation Method | |
Electrostatic and van der Waals | |
Electrostatic | Group Based |
van der Waals | Group Based |
Apply Long Range Correction | True |
Atom Cutoff Distance | 12.5 |
Atom Spline Width | 1.0 |
Calculate Charge Groups | True |
Total Charge Tolerance | 0.1 |
Charge Group Assignment Method | Divide and Conquer |
Charge Group Cutoff Distance | 10 |
Charge Group Spline Width | 1.0 |
Electrostatic Ewald Accuracy | 1.e-3 |
Electrostatic PPPM Accuracy | 1.e-3 |
van der Waals Ewald Accuracy | 1.e-3 |
Ewald Repulsive Cutoff | 12 |
Buffer Width | 0.5 |
Hydrogen Bond | |
Hydrogen Bond Atom Cutoff Distance | 4.5 |
Hydrogen Bond Atom Spline Width | 0.5 |
Hydrogen Bond Buffer Width | 0.5 |
Parallel | |
Parallel Server | crater.a04.aist.go.jp |
Parallel Queue | |
Parallel Threads | 36 |
Error.txt follows:
Error executing parallel subprotocol on crater.a04.aist.go.jp: 'Unable to find bond to delete at (eval 10) line 112.'
main::RingOpening(Cfx::COM=HASH(0xd12dcf8), Cfx::COM=HASH(0x7756560)) called at (eval 10) line 32
main::onProcess
Error calling function
Error during call to function pilot::setup::scriptingOnProcess
PerlScript::HandleError: Pipeline Pilot exception rethrown
PerlScript::Call: Pipeline Pilot exception rethrown
CComponentPerlPlugin::onProcess: Pipeline Pilot exception rethrown
-> 'Perl (on Server)' ('Perl (on Server)'); Location: 0:71:60:0:1:0 - error during Data Record Processing phase
CProtocolStd::onProcess: Pipeline Pilot exception rethrown
CProtocol::onProcess: Pipeline Pilot exception rethrown
-> 'Subprotocol' ('Subprotocol 1'); Location: 0:71:60:0:1 - error during Data Record Processing phase
CProtocolStd::onProcess: Pipeline Pilot exception rethrown
CProtocol::onProcess: Pipeline Pilot exception rethrown
-> 'Perl MaterialsScript (on Server)' ('Perl MaterialsScript (on Server)'); Location: 0:71:60:0 - error during Data Record Processing phase
CProtocolStd::onProcess: Pipeline Pilot exception rethrown
CProtocol::onProcess: Pipeline Pilot exception rethrown
-> 'Subprotocol' ('Perform Reaction'); Location: 0:71:60 - error during Data Record Processing phase
CProtocolRtc::onProcess: Pipeline Pilot exception rethrown
CProtocol::onProcess: Pipeline Pilot exception rethrown
-> 'Subprotocol' ('Reaction cycle'); Location: 0:71 - error during Data Record Processing phase
CProtocolStd::onProcess: Pipeline Pilot exception rethrown
CProtocol::onProcess: Pipeline Pilot exception rethrown
-> 'Subprotocol' ('subprotocol template'); Location: 0 - error during Data Record Processing phase
CProtocolStd::onProcess: Pipeline Pilot exception rethrown
CProtocol::onProcess: Pipeline Pilot exception rethrown
CComponentRunner::CallOnProcess: exception caught, calling onFinalize before rethrow
Protocol Create Polymer Network fixed/Cross linking, user pfons: Pipeline Pilot exception caught
Protocol Create Polymer Network fixed/Cross linking, user pfons: Protocol failed: Pipeline Pilot error
Pipeline Pilot Server version 18.1.100.11
Server OS: Linux crater.a04.aist.go.jp 3.10.0-327.28.3.el7.x86_64 #1 SMP Thu Aug 18 19:05:49 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
CRemoteProtocol::CProtocolBatch::HandleError: Pipeline Pilot exception rethrown
CRemoteProtocol::CProtocolBatch::HandleCompletion: Pipeline Pilot exception rethrown
CRemoteProtocol::CBatchMonitorThread::ResolveCompletedBatch: Pipeline Pilot exception caught
CRemoteProtocol::CBatchMonitorThread::ResolveCompletedBatches: Pipeline Pilot exception rethrown
CRemoteProtocol::onProcess: Pipeline Pilot exception rethrown
CProtocol::onProcess: Pipeline Pilot exception rethrown
-> 'Subprotocol' ('Cross linking'); Location: 106:0 - error during Data Record Processing phase
CProtocolStd::onProcess: Pipeline Pilot exception rethrown
CProtocol::onProcess: Pipeline Pilot exception rethrown
-> 'Subprotocol' ('Cross linking'); Location: 106 - error during Data Record Processing phase
CProtocolStd::onProcess: Pipeline Pilot exception rethrown
CProtocol::onProcess: Pipeline Pilot exception rethrown
CComponentRunner::CallOnProcess: exception caught, calling onFinalize before rethrow
Protocol Create Polymer Network fixed, user pfons: Pipeline Pilot exception caught
Protocol Create Polymer Network fixed, user pfons: Protocol failed: Pipeline Pilot error
Pipeline Pilot Server version 18.1.100.11
Server OS: Linux crater.a04.aist.go.jp 3.10.0-327.28.3.el7.x86_64 #1 SMP Thu Aug 18 19:05:49 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
