I have a weird problem occurring. I run my system (graphite + water @
1g/cm3 + peptide) in Windows and it converts just fine from CIF to XYZ.
The system is about 2,346 atoms big and periodic (but that doesn't really
matter going to XYZ). In Windows, the program converts just like it
should, no errors or anything, but when I try to use the Linux version it
continues to run without completing. I finally ran it in debug mode and
below is the output:
==============================
*** Open Babel Audit Log in ReadChemObjectImpl
OpenBabel::Read molecule Crystallographic Information File
==============================
*** Open Babel Audit Log in ConnectTheDots
Ran OpenBabel::ConnectTheDots
==============================
*** Open Babel Audit Log in PerceiveBondOrders
Ran OpenBabel::PerceiveBondOrders
==============================
*** Open Babel Audit Log in FindSSSR
Ran OpenBabel::FindSSSR
==============================
*** Open Babel Audit Log in FindRingAtomsAndBonds
Ran OpenBabel::
FindRingAtomsAndBonds
==============================
*** Open Babel Audit Log in IsClosure
Ran OpenBabel::PerceiveClosureBonds
==============================
*** Open Babel Audit Log in AssignAromaticFlags
Ran OpenBabel::AssignAromaticFlags
==============================
*** Open Babel Audit Log in AssignImplicitValence
Ran OpenBabel::AssignImplicitValence
==============================
*** Open Babel Audit Log in Kekulize
Ran OpenBabel::Kekulize
It looks like it's hanging up at this point, because it doesn't do anything
else until the Supercomputer Administrators get mad at me for running on
the head node and kill it. I'm currently running in my own Linux Box, but
I'm still stuck at the same place and it has been running for about 30
minutes now (and only took about 30 seconds in Windows). Any help you can
give me would be greatly appreciated.
Regards,
David Cossey
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