delphi 7.0 and lates reduce fail in delphiBindingEnergy.py

[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)

[neb9]

I don't know very much about how Biskit deals with Delphi, but I do notice that there seems to be a problem with removing the temp directory. Is it possible that your permissions are improperly set? I don't think this is contributing to the other error, but it's worth checking.

[parashardhapola]

The problem got fixed when using older version of Delphi. Probably the output of Delphi 7 is not what Biskit looks for and treats it as error.

[graik]

Thanks for reporting. I have not yet tested the wrapper with Delphi 7.0 which seems to be a complete re-write. From the backtrace, I see two issues: the warning about missing hydrogens should be taken seriously because it will obviously affect the calculation heavily. This could point to some issue with reduce. The eventual failure is probably triggered because the "success" message from delphi has changed. So that could be adapted easily. I'll see how far we get with delphi95 and AmberTools 16 reduce and then take it from there. Greetings Raik

…

On Tue, Jan 3, 2017 at 1:24 PM, Parashar ***@***.***> wrote: Closed #17 <#17>. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#17 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABxs3TSMnCDc0ctblz0Rzob3xsdVWAbXks5rOkv8gaJpZM4LZMGM> .

--

___________________________________ Raik Grünberg http://www.raiks.de/contact.html

___________________________________

[graik]

This report may point to an issue with the latest version of reduce as well as Delphi 7.0