Re: [Open Babel] from mol to mop

2012-04-25 Thread Noel O'Boyle
Hi Marie-Noƫlle, What exactly is T.E.S.T.? Google cannot find it. Without knowing, I'm guessing that you made a 2D structure. MOPAC requires a 3D structure. Try using --gen3D to make a 3D structure. If there is still a problem, it means that OB has gotten the units confused, and it's a bug on ou

[Open Babel] from mol to mop

2012-04-25 Thread Marie-Noelle Pons
Hi, I am new in using tools such as babel and mopac. I am first running a small test on formaldehyde. I have designed the mol file using T.E.S.T. from US EPA, then used babel to get from .mol to .mop in cartesian units. Now when I run mopac, some atoms are too close one from the other. I cannot

Re: [Open Babel] Why this happening? using ob.py from html

2012-04-25 Thread Igor Filippov
Park, You have LD_LIBRARY_PATH set up for your shell which the webserver known nothing about. You should set up LD_LIBRARY_PATH for the apache (or whatever httpd daemon you have) process. I would do this in the script itself before importing openbabel module. Igor On Wed, 2012-04-25 at 03:16 -0

Re: [Open Babel] Why this happening? using ob.py from html

2012-04-25 Thread Park Hyerin
Solve problem! This problem didn't relate with openbabel setting. I wonder if someone have a trouble like this, I wrote how to solve this problem. At first... Do this on command line # vi /etc/ld.so.conf And add this line in ld.so.conf /usr/local/lib And the final step, adapting change. # /sbin/

Re: [Open Babel] Why this happening? using ob.py from html

2012-04-25 Thread Park Hyerin
Thanks for your advice. I checked web server error log and I found this message. [error] [client xxx.xxx.xxx.xx] ImportError: libopenbabel.so.4: cannot open shared object file: No such file or directory, referer: --.html So I tried to fix this error and I found this error related with LD_LI