MMTSB
Tool Set Documentation

Installation

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Revision as of 13:28, 6 July 2009 by Edit (Talk | contribs) (Troubleshooting)

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Unpacking

To install, go to the directory where you want to install the package (e.g. /usr/local) and unpack with

  gzip -d <package>.tar.gz
  tar xvf <package>.tar

This will create all files in the current directory

Now start the installation with

  ./install.sh

After running the installation script compiled binaries are available in ./bin and self-starting perl scripts are in ./perl. Related data files are in ./data and examples for each perl script are under ./bench.

Setup

Every user planning to use the MMTSB tools should set the environment variable MMTSBDIR to the directory where the MMTSB tools are installed (e.g. /usr/local) and include $MMTSBDIR/bin and $MMTSBDIR/perl in the file search path as follows:

For csh/tcsh:

 setenv MMTSBDIR <installation-dir>
 set path = ( $path $MMTSBDIR/perl $MMTSBDIR/bin )

and for sh/bash:

 export MMTSBDIR = <installation-dir>
 export PATH = $PATH:$MMTSBDIR/perl:$MMTSBDIR/bin

For parallel execution, you may also specify the program for remote login without passwords in REMOTESHELL, e.g.:

 setenv REMOTESHELL rsh

Integration with other packages

The MMTSB Tool Set benefits from the availability of other software packages, in particular CHARMM, Amber, Modeller, DSSP, SCWRL, NCBI-BLAST, PSIPRED.

The following environment variables are related to these packages and should be set accordingly:

 CHARMMEXEC    CHARMM executable
 CHARMMDATA    CHARMM data files
 AMBERHOME     Amber installation directory
 SANDEREXEC    Amber sander executable
 LEAPEXEC      Amber tLeap executable
 MODELLEREXEC  Modeller executable
 PSIPREDDIR    PSIPRED installation directory
 PDBDIR        Directory with local copy of PDB 

Troubleshooting

Perl

Perl 5.004 or newer is required to run the perl scripts. All perl scripts check whether this (or a newer) version is available and and will abort with a message if not. /usr/bin/env is used to find the location of perl. This works only if perl can be found in the search path. An error like

 env: perl: No such file or directory

indicates that perl is either not installed or its location is not included in the search path. Binary and source code distributions of latest perl versions are available through http://www.cpan.org


Compiling

The provided Makefile uses gcc, g++, and g77 to compile the binaries. If that is not appropriate for your platform or special linker options are needed, the file src/Makefile needs to be modified accordingly. Please consult your local system administrator if necessary.

Using Mac OSX

The following environment variables must be assigned, otherwise MMSTB commands that access CHARMMEXEC will hang:

export GFORTRAN_UNBUFFERED_ALL=y #required to give unbuffered io with gfortran
export G95_UNBUFFERED_ALL=y #required to give unbuffered io with g95

Running

If problems occur with running the scripts or programs please consult the documentation at http://feig.bch.msu.edu/mmtsb and check your input data.