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Description
Error log:
Reduce version 3.23
Delphi version 7.0
test_bindingE (__main__.Test)
bindingEnergyDelphi test (Barnase:Barstar) ...
Re-building hydrogen atoms...
executing: /home/parashar/software/reduce_3.23.130521.linuxi386/reduce -BUILD -Nterm2 -DB /home/parashar/software/biskit/Biskit/data/reduce/reduce_wwPDB_het_dict.txt /tmp/reduce_HvDdqn_in.pdb
in folder: None
input: None
output: <open file '/tmp/reduce_4T_9c7_out.pdb', mode 'w' at 0x7f8f7187fb70>
errors: <open file '/tmp/reduce_zswu1P.err', mode 'w' at 0x7f8f7187fc00>
wrapped: 0
shell: None
environment: None
.. finished.
Assigning charges from Amber topologies...
parsing all_amino03.in...
Read 33 residue definitions.
parsing all_aminoct03.in...
Read 22 residue definitions.
parsing all_aminont03.in...
Read 22 residue definitions.
parsing all_nuc02.in...
Read 37 residue definitions.
Delphi calculations with 0.150 M salt
=======================================
running Delphi for complex...
creating temporary directory /tmp/delphi_Ing4WF
Creating Delphi charge file /tmp/delphi_Ing4WF/delphi_Y7wKHq.crg
Atoms without charges: 0
executing: /home/parashar/software/Delphi_Linux/executable/delphi /tmp/delphi_Ing4WF/delphi_UQRThO.inp
in folder: /tmp/delphi_Ing4WF
input: <open file '/tmp/delphi_Ing4WF/delphi_UQRThO.inp', mode 'r' at 0x7f8f7187fc00>
output: <open file '/tmp/delphi_Ing4WF/delphi_yvotaS.out', mode 'w' at 0x7f8f7187fb70>
errors: <open file '/tmp/delphi_Ing4WF/delphi_5AL2Dp.err', mode 'w' at 0x7f8f7187fc90>
wrapped: 0
shell: None
environment: None
.. finished.
Delphi failed. Please check the program output in the field `output` of this Delphi instance (e.g. `print x.output`)!
The last message from DelPhi reads as follows:
......... PROGRAM EXITS SUCCESSFULLY : WITH TOTAL 3473 WARNING(S) ........
Removing non-empty temporary folder /tmp/delphi_Ing4WF
ERROR
test_errorcase1 (__main__.Test)
bindinEnergyDelphi test (error case 01) ...
Re-building hydrogen atoms...
executing: /home/parashar/software/reduce_3.23.130521.linuxi386/reduce -BUILD -Nterm3 -DB /home/parashar/software/biskit/Biskit/data/reduce/reduce_wwPDB_het_dict.txt /tmp/reduce_goTDxO_in.pdb
in folder: None
input: None
output: <open file '/tmp/reduce_qKoQGa_out.pdb', mode 'w' at 0x7f8f7187fdb0>
errors: <open file '/tmp/reduce_gq23ed.err', mode 'w' at 0x7f8f7187fc90>
wrapped: 0
shell: None
environment: None
.. finished.
Assigning charges from Amber topologies...
parsing all_amino03.in...
Read 33 residue definitions.
parsing all_aminoct03.in...
Read 22 residue definitions.
parsing all_aminont03.in...
Read 22 residue definitions.
parsing all_nuc02.in...
Read 37 residue definitions.
Warning: 1 atoms missing from residue #0 (VAL 74 A):
['H']
Ignored. Residue will have incomplete charge.
Warning: 1 atoms missing from residue #75 (GLU 179 A):
['H']
Ignored. Residue will have incomplete charge.
Warning: 1 atoms missing from residue #100 (THR 71 B):
['H']
Ignored. Residue will have incomplete charge.
Warning: 1 atoms missing from residue #178 (GLU 179 B):
['H']
Ignored. Residue will have incomplete charge.
Warning: 1 atoms missing from residue #203 (THR 85 C):
['H']
Ignored. Residue will have incomplete charge.
Delphi calculations with 0.150 M salt
=======================================
running Delphi for complex...
creating temporary directory /tmp/delphi_8h4Cwr
Creating Delphi charge file /tmp/delphi_8h4Cwr/delphi_AZ4ghY.crg
Atoms without charges: 0
executing: /home/parashar/software/Delphi_Linux/executable/delphi /tmp/delphi_8h4Cwr/delphi_Z8qteD.inp
in folder: /tmp/delphi_8h4Cwr
input: <open file '/tmp/delphi_8h4Cwr/delphi_Z8qteD.inp', mode 'r' at 0x7f8f7187fc90>
output: <open file '/tmp/delphi_8h4Cwr/delphi_Q1UFAk.out', mode 'w' at 0x7f8f7187fdb0>
errors: <open file '/tmp/delphi_8h4Cwr/delphi_2_cvol.err', mode 'w' at 0x7f8f7187fb70>
wrapped: 0
shell: None
environment: None
.. finished.
Delphi failed. Please check the program output in the field `output` of this Delphi instance (e.g. `print x.output`)!
The last message from DelPhi reads as follows:
......... PROGRAM EXITS SUCCESSFULLY : WITH TOTAL 4774 WARNING(S) ........
Removing non-empty temporary folder /tmp/delphi_8h4Cwr
ERROR
======================================================================
ERROR: test_bindingE (__main__.Test)
bindingEnergyDelphi test (Barnase:Barstar)
----------------------------------------------------------------------
Traceback (most recent call last):
File "delphiBindingEnergy.py", line 431, in test_bindingE
self.r = self.dG.run()
File "delphiBindingEnergy.py", line 397, in run
self.ezero, self.esalt = self.processSixsome()
File "delphiBindingEnergy.py", line 327, in processSixsome
ri_com, ri_rec, ri_lig = self.processThreesome( salt=self.salt, **kw )
File "delphiBindingEnergy.py", line 304, in processThreesome
r_com = dcom.run()
File "/home/parashar/software/biskit/Biskit/Executor.py", line 555, in run
self.fail()
File "/home/parashar/software/biskit/Biskit/delphi.py", line 600, in fail
raise DelphiError, s
DelphiError: The last message from DelPhi reads as follows:
......... PROGRAM EXITS SUCCESSFULLY : WITH TOTAL 3473 WARNING(S) ........
======================================================================
ERROR: test_errorcase1 (__main__.Test)
bindinEnergyDelphi test (error case 01)
----------------------------------------------------------------------
Traceback (most recent call last):
File "delphiBindingEnergy.py", line 449, in test_errorcase1
self.r = self.dG.run()
File "delphiBindingEnergy.py", line 397, in run
self.ezero, self.esalt = self.processSixsome()
File "delphiBindingEnergy.py", line 327, in processSixsome
ri_com, ri_rec, ri_lig = self.processThreesome( salt=self.salt, **kw )
File "delphiBindingEnergy.py", line 304, in processThreesome
r_com = dcom.run()
File "/home/parashar/software/biskit/Biskit/Executor.py", line 555, in run
self.fail()
File "/home/parashar/software/biskit/Biskit/delphi.py", line 600, in fail
raise DelphiError, s
DelphiError: The last message from DelPhi reads as follows:
......... PROGRAM EXITS SUCCESSFULLY : WITH TOTAL 4774 WARNING(S) ........
----------------------------------------------------------------------
Ran 2 tests in 31.733s
FAILED (errors=2)