MMTSB Toolset installation

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MMTSB stands for Multiscale Modeling Tools for Structural Biology. It is a novel collection of utilities and programming libraries that enable the simulation of proteins and nucleic acids to use advanced sampling and multiscale modelling techniques. For classical all-atom simulations, the tool set interacts with the current molecular modelling packages CHARMM and Amber, and with MONSSTER for lattice-based low-resolution conformational sampling. The tool set is intended for structural biology applications that need the prediction, refining, and/or extended conformational sampling of protein or nucleic acid structures. It also incorporates an ensemble computing capability that enables the control and execution of modelling tasks on a broad range of conformations. For Further details the links are given below.


Installation instructions for centos 7:

1. The package is available on GITHUB: https://github.com/mmtsb/toolset

#From here download the zip file from the "code" option.

2. To install, unzip the folder. Then:

cd toolset-master

cd src

make all

3. Add the path in bash file

vi ~/.bashrc

#add the following two commands in the bashrc:

export MMTSBDIR=/home/user/Downloads/toolset-master

export PATH=$PATH:$MMTSBDIR/perl:$MMTSBDIR/bin

save the bashrc (:wq!)

4.  in your working directory (i.e. go to the folder where you want to use the package) open the terminal and type the following. # you need to source the bashrc once in the terminal and perform the job in the same terminal.

source ~/.bashrc

5. check whether it is running or not:

You may determine this by looking at the value of the environment variable MMTSBDIR. E.g. 

echo $MMTSBDIR # this will show that the path of the package is set.

or 

type kclust (or any module name) and then enter .. an empty next line should come.

or else, if this doesn't come then you need to give the full path of that module present in the bin.

/home/user/Downloads/toolset-master/bin/kclust



Useful links/references:

http://feig.bch.msu.edu/mmtsb/Main_Page

https://pubmed.ncbi.nlm.nih.gov/15099834/

https://ambermd.org/tutorials/basic/tutorial3/section6.htm


For any queries, kindly drop your message in the comments section below.

Please also provide your valuable feedback and stay tuned for more such blogs and scripts!!

Happy Computing!!



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