Hi,
We are using obabel to perform geometry optimizations etc on the
command line, and we are hitting a bug that seems to only present
itself on the Mac. If the input and output formats are the same then
the operation fails, for example,
obabel -icml -ocml --minimize --log --ff UFF
That is using standard in/out, but it also seems to happen when using
files. This works as expected on Linux and Windows, are we diverging
from expected use too much or is this a bug. This is the same in 2.3.2
and master, using 10.6.8 and GCC 4.2.1.
The full output is below, compared with using xyz as the output (we
could of course work around this issue by using different formats).
There is a SMARTS error I just noticed too, but that seems unrelated
to this bug on the Mac.
$ obabel -icml ethane.cml -ocml --minimize --log --ff UFF
==============================
*** Open Babel Error in RegisterOptionParam
The number of parameters needed by option "t" in The LPMD file
format. differs from an earlier registration.
==============================
*** Open Babel Error in SMARTSError
SMARTS Error:
[#6+:1](~N:2)(~N:3)*
^
A T O M T Y P E S
IDX TYPE RING
1 H_ NO
2 C_3 NO
3 H_ NO
4 H_ NO
5 C_3 NO
6 H_ NO
7 H_ NO
8 H_ NO
S E T T I N G U P C A L C U L A T I O N S
SETTING UP BOND CALCULATIONS...
SETTING UP ANGLE CALCULATIONS...
SETTING UP TORSION CALCULATIONS...
SETTING UP OOP CALCULATIONS...
SETTING UP VAN DER WAALS CALCULATIONS...
C O N J U G A T E G R A D I E N T S
STEPS = 2500
STEP n E(n) E(n-1)
--------------------------------
1 2.378 4.699
4 1.069 1.069
CONJUGATE GRADIENTS HAS CONVERGED
0 molecules converted
$ obabel -icml ethane.cml -oxyz --minimize --log --ff UFF
==============================
*** Open Babel Error in RegisterOptionParam
The number of parameters needed by option "t" in The LPMD file
format. differs from an earlier registration.
==============================
*** Open Babel Error in SMARTSError
SMARTS Error:
[#6+:1](~N:2)(~N:3)*
^
A T O M T Y P E S
IDX TYPE RING
1 H_ NO
2 C_3 NO
3 H_ NO
4 H_ NO
5 C_3 NO
6 H_ NO
7 H_ NO
8 H_ NO
S E T T I N G U P C A L C U L A T I O N S
SETTING UP BOND CALCULATIONS...
SETTING UP ANGLE CALCULATIONS...
SETTING UP TORSION CALCULATIONS...
SETTING UP OOP CALCULATIONS...
SETTING UP VAN DER WAALS CALCULATIONS...
C O N J U G A T E G R A D I E N T S
STEPS = 2500
STEP n E(n) E(n-1)
--------------------------------
1 2.378 4.699
4 1.069 1.069
CONJUGATE GRADIENTS HAS CONVERGED
8
Ethane
H 1.17997 -0.00310 1.00769
C 0.76583 -0.02288 -0.02125
H 1.16144 0.85024 -0.57962
H 1.10906 -0.95033 -0.52388
C -0.76582 0.02291 0.02127
H -1.16141 -0.85054 0.57913
H -1.10918 0.95009 0.52435
H -1.17989 0.00361 -1.00770
1 molecule converted
------------------------------------------------------------------------------
Precog is a next-generation analytics platform capable of advanced
analytics on semi-structured data. The platform includes APIs for building
apps and a phenomenal toolset for data science. Developers can use
our toolset for easy data analysis & visualization. Get a free account!
http://www2.precog.com/precogplatform/slashdotnewsletter
_______________________________________________
OpenBabel-Devel mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/openbabel-devel
