[AMBER] MMPBSA.py install error

From: Catein Catherine <askamber23.hotmail.com>
Date: Sat, 3 Jul 2010 19:38:33 +0800

Dear Amber Experts,


I could like to install MMPBSA.py. Following the discriptions in the tutorial. I do the followings things, but error message at the end of this email was encountered. Could you mind to teach me how to get rid of this?


(1) Download python2.6.5 in my linux workstation. I extract the file in /home directory. type "./configure" in /home/python2.6.5 directory. type "make", This creates an executable "./python" to install in /usr/local directory. Then I type "sudo make install"


(2) I found Numberic, Numeric.path and README files in the /usr/local/lib/python2.6.5/site-packages/ directory.



(5) in home directory of the console. I typed


"export PYTHONPATH=/home/user/lib/python2.6.5/site-packages\:$PYTHONPATH


(3) When I type python. I see follows:

'import site' failed; use -v for traceback
Python 2.6.5 (r265:79063, Jul 3 2010, 18:49:13)
[GCC 4.4.1] on linux2
Type "help", "copyright", "credits" or "license" for more information.


(5) I "think" python 2.6.5 was installed.


(6) Then, I process to install MMPBSA.py for serial runs.


(7) mv mm_pbsa_py.tar.gz $AMBERHOME/src


(8) tar zxvf mmpbsa_py.tar.gz


(9) cd $AMBERHOME/src/mmpbsa_py


(10) make serial clean to make sure it is a clean installation.


(11) I found following error message when after installation


/bin/bash setup.sh
Python version 2 detected. No file conversion necessary.
'import site' failed; use -v for traceback
/bin/cp MMPBSA.py *pyc /home/amber10/bin
/home/amber10/bin/nab -o mmpbsa_py_nabnmode mmpbsa_entropy. nab
mmpbsa_entropy.nab:58 fld 'ls_method' not in struct 'xo'
mmpbsa_entropy.nab:58 operator '=': left operand has wrong class.
mmpbsa_entropy.nab:58 unknown attribute 'ls_method'
mmpbsa_entropy.nab:59 fld 'ls_maxiter' not in struct 'xo'
mmpbsa_entropy.nab:59 operator '=': left operand has wrong class.
mmpbsa_entropy.nab:59 unknown attribute 'ls_maxiter'
mmpbsa_entropy.nab:60 fld 'ls_maxatmov' not in struct 'xo'
mmpbsa_entropy.nab:60 operator '=': left operand has wrong class.
mmpbsa_entropy.nab:60 unknown attribute 'ls_maxatmov'
nab2c failed!
make: [install] Error 1 (ignored)
/bin/mv mmpbsa_py_nabnmode /home/amber10/bin
/bin/mv: cannot stat `mmpbsa_py_nabnmode': No such file or directory
make: [install] Error 1 (ignored)
/bin/rm -f *pyc
/bin/rm -f mmpbsa_entropy.c


(15) I saw the executable file MMPBSA.py in the /home/amber10/src/mmpbsa_py directory. I then type MMPBSA.py in the same directory



'import site' failed; use -v for traceback
Traceback (most recent call last):
  File "/home/amber10/exe/MMPBSA.py", line 42, in <module>
    import sys, os, time, math # (1)
ImportError: No module named os


(16) I tried to type MMPBSA.py in the /home/amber10/exe directory. However, the same error message was found.


Did I do anything wrong here? Did I miss any important steps. Please kindly instruct.


Best regards,


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Received on Sat Jul 03 2010 - 05:00:02 PDT
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