Thanks Jason,
I tried what you said
cgaughan.tg-login1:~/2psj_A/2psj_A_CTZ/2psj_2ctz_112812/mmpbsa/ante_mmpbsa> python -c "import math"
cgaughan.tg-login1:~/2psj_A/2psj_A_CTZ/2psj_2ctz_112812/mmpbsa/ante_mmpbsa> ante-MMPBSA.py -p ./2psj_2ctz_112812.prmtop -c ./complex_unsolvated.prmtop -r receptor.prmtop -l ligand.prmtop -s ":WAT,Na+" -m ":1-306"
Stripping :WAT,Na+ (solvent) from original topology, output is ./complex_unsolvated.prmtop
Error: Creating complex topology failed!
Traceback (most recent call last):
File "/usr/local/packages/AMBER12/parmed.py", line 5, in <module>
import sys, math
ImportError: /usr/local/packages/yt-x86_64/lib/python2.7/lib-dynload/math.so: undefined symbol: PyLong_AsLongAndOverflow
but got the same result. I'm working on the Blacklight cluster (XSEDE) so I can't fix python. Maybe I can ask them to re-install it.
Chris
________________________________
From: Jason Swails <jason.swails.gmail.com>
To: Chris Chris <alpharecept.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Friday, April 19, 2013 11:07 AM
Subject: Re: [AMBER] ante-MMPBSA.py problem
On Fri, Apr 19, 2013 at 12:56 PM, Chris Chris <alpharecept.yahoo.com> wrote:
> I have been having trouble with topology files when using mmpbsa_mpi.py
>
> To hopefully get around the problem, I am using ante-MMPBSA.py.
>
> Can someone tell me what I'm doing wrong here?
>
> cgaughan.tg-login1:~/2psj_A/2psj_A_CTZ/2psj_2ctz_112812/mmpbsa/ante_mmpbsa>
> ante-MMPBSA.py -p ./2psj_2ctz_112812.prmtop -c ./complex_unsolvated.prmtop
> -r receptor.prmtop -l ligand.prmtop -s ":WAT" -s ":Na+" -m ":1-306"
> Stripping :Na+ (solvent) from original topology, output is
> ./complex_unsolvated.prmtop
> Error: Creating complex topology failed!
>
You can only specify one strip mask. This will only strip Na+ ions (as the
message tells you). If you want to strip both water and Na+, you need to
use:
-s ":WAT,Na+"
>
> Traceback (most recent call last):
> File "/usr/local/packages/AMBER12/parmed.py", line 5, in <module>
> import sys, math
> ImportError:
> /usr/local/packages/yt-x86_64/lib/python2.7/lib-dynload/math.so: undefined
> symbol: PyLong_AsLongAndOverflow
>
Your Python appears to be broken. Try this command:
python -c "import math"
If you get an error message, see if there is another Python installed on
your system and try that one instead (via the --with-python
/your/new/python flag to configure). I'm afraid we will not be able to
help you debug a problem with your Python installation (we would just tell
you to re-install Python).
If you get no error message (it should appear to do nothing), then look at
the first line of your $AMBERHOME/bin/ante-MMPBSA.py file. It should look
something like:
#!/usr/local/packages/yt-x86_64/bin/python2.7
or something like that. Then run the same test on that python:
/usr/local/packages/yt-x86_64/bin/python2.7 -c "import math"
That should give you an error. If you got no error with the first command,
then you can re-install AmberTools using this system-default Python and
that should fix your issue. (Basically just go to $AMBERHOME and run
./configure gnu again).
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Apr 19 2013 - 23:30:03 PDT
