TEN (Tools for Elastic Networks)
Two versions of the Elastic Network Model, the Gaussian Network Model (GNM) and the Anisotropic Network Model (ANM) are implemented.If you are using any of the software connected to CoMoDo. please cite:
- Silke A. Wieninger and G. Matthias Ullmann.
CoMoDo: Identifying Dynamic Protein Domains Based on Covariances of Motion.
J. Chem. Theory Comput. B, 11: 2841-2854, 2015
[PDF File] [Supporting Informations]
Usage
The TEN package consists of three programs:
- EValVecC: calculates eigenvalues and -vectors (normal modes)
- NWAnalyzer: calculates covariances, correlations and theoretical B-factors
- MovieGenerator: computes trajectories from normal modes
The protein structure must be given in pqrm format.
Download
Download the file TEN.tar.gz
The program is available under the Gnu Affero Public License. The package includes
- C++ code of EValVecC, NWAnalyzer and MovieGenerator
- Makefile
- Example files
Installation
TEN requires the following packages:
- BOOST C++ Libraries (boost_1_56_0)
doesn't have to be build, just download and unpack - LAPACK Linear Algebra PACKage (lapack-3.5.0)
some hints for the installation:
cp INSTALL/make.inc.gfortran make.inc
changes to make.inc: flag -fPIC: create position independent code needed for shared libraries
OPTS -02 -frecursive -fPIC
NOOPT -02 -frecursive -fPIC
BLASLIB=../../libblas.a
cd BLAS/SRC
make
cd ../../
make
make install - LAPACK++ (lapackpp-2.5.4)
./configure --prefix=$PATH/lapackpp-2.5.4 --with-blas=$PATH/lapack-3.5.0/libblas.a --with-lapack=$PATH/lapack-3.5.0/liblapack.a (--enable-static=yes) --enable-atlas=no
make
make install
Installation of TEN:
- Download the file TEN.tar.gz
- Type
tar -jxf TEN.tar.gz
- Go to the directory TEN:
cd TEN
- Change the settings in Makefile.rules, esp. the library paths
- Type
make
LD_LIBRARY_PATH
:
- in sh:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$PATH/lapackpp-2.5.4/lib
- in csh:
setenv LD_LIBRARY_PATH $LD_LIBRARY_PATH:$PATH/lapackpp-2.5.4/lib
Other ENM programs
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