8000 delphi 7.0 and lates reduce fail in delphiBindingEnergy.py · Issue #17 · graik/biskit · GitHub
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delphi 7.0 and lates reduce fail in delphiBindingEnergy.py #17
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@parashardhapola

Description

@parashardhapola

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)

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