[MMTK] Fwd:Normal modes -error

Mohan maruthi sena maruthi.sena at gmail.com
Tue Dec 11 06:13:27 UTC 2012

Hi all,
            I could install MMTK by the changing the path
trajectory.h/Scientific/netcdf.h. Now I want to calculate normal modes for
a given protein. I following the example given in MMTK site. When I use
those commands I get the following error:

*from* MMTK *import* *

*from* MMTK.Proteins *import* Protein
*from* MMTK.ForceFields *import* Amber94ForceField
*from* MMTK.NormalModes *import* NormalModes

from MMTK.Minimization import ConjugateGradientMinimizer
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/local/lib/python2.6/dist-packages/MMTK/Minimization.py", line
13, in <module>
    from MMTK import Features, ThreadManager, Trajectory, Units
  File "/usr/local/lib/python2.6/dist-packages/MMTK/Trajectory.py", line
24, in <module>
    "because the netCDF module is missing.")
MMTK.Utility.MMTKError: Trajectories are not available because the netCDF
module is missing.

I have netCDF installed in my system. I use python 2.6.6. Can anyone please
help me to understand this error.

Thanking you in advance,

---------- Forwarded message ----------
From: Mohan maruthi sena <maruthi.sena at gmail.com>
Date: Tue, Dec 11, 2012 at 10:22 AM
Subject: Installation problems -MMTK- ubuntu 10.10
To: mmtk <mmtk at starship.python.net>

Hello Sir,
                 I want to install MMTK  in my system but when run the
command ' python setup.py build' , I get the following error as shown below:

config/intlen.c: In function ‘main’:
config/intlen.c:6: warning: format ‘%d’ expects type ‘int’, but argument 2
has type ‘long unsigned int’
running build
running build_py
running build_ext
building 'MMTK_DCD' extension
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall
-IInclude -I/usr/lib/python2.6/site-packages/numpy/core/include
-I/usr/include/python2.6 -c Src/MMTK_DCD.c -o
build/temp.linux-x86_64-2.6/Src/MMTK_DCD.o -DUSE_NETCDF_H_FROM_SCIENTIFIC=1
In file included from Src/MMTK_DCD.c:9:
Include/MMTK/trajectory.h:15: fatal error: Scientific/netcdf.h: No such
file or directory
compilation terminated.
error: command 'gcc' failed with exit status 1

Can anyone please suggest me a way to rectify this.

Thanking you in advance,
K.Mohan Maruthi
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