Getting Started

Download and Installation procedure

Currently the download is freely available at - https://github.com/ZuckermanLab/mrmc.git

One can freely download the zip file from the above site or clone it by using the following command on terminal - git clone https://github.com/ZuckermanLab/mrmc.git

The installation procedure is quite simple, after downloading the mrmc code from the above site, extract it into a desired directory.

The code may be compiled using the compile script that is provided. To produce a plain, optimized version of the code, simply invoke the compile script without arguments. The compilation uses the Intel C++ compiler or the GNU g++ compiler. The script takes arguments that indicate conditional compiler directives to be used. Adding the timers argument creates a special version that outputs timing data on individual parts of the calculation. By default the script also applies a conditional compiler directive that selects the force field. The choices are AMBER and CHARMM19. By default AMBER is applied; this can be changed within the script. The CHARMM19 selection should work, but has not been tested recently.

Go to the mrmc/ directory and then get into the src/ directory and type the following command in the terminal - ./compile

This command will compile all the .cpp files present in the src/ folder and will generate *.o files. The mrmc file generated is now used to run the simulation, one can either keep them with the other binaries or give its path to wherever running the simulation.

Adding the debug argument creates a debuggable version with disabled optimization that produces lots of extra output.

To debug , type - ./compile debug

Running the code - mrmc input-file.txt >output-file.txt

#Minimal Pre-requisites for running the code -

1. Python - https://www.python.org/downloads/ (numpy should be installed along with this)

2. Some Python modules - a. ParmED - https://github.com/ParmEd/ParmEd/releases b. networkx - https://networkx.github.io/documentation/development/install.html

3. Open babel - https://openbabel.org/docs/dev/Installation/install.html#linux

4. Amber Tools -http://ambermd.org/#AmberTools

After installing the above packages, mrmc should run fine but if you still have any problems then feel free to notify us.

Using the input :

One can run the input file (example-go-input.txt) given along side the code by typing the following into the terminal and save its output to another file-

./mrmc example-go-input.txt > output-file

For this please copy executable mrmc generated to the directory containing the input file or otherwise give the path accordingly.

The input commands are explained in another section names - "Input Commands"

For Ligand parameterization, one will need the sdf / sdf&pdb file of the ligand that can be obtained from the various databanks provided online. Then use the file setup-no-pdb(if you don't have the pdb of the crystal structure) or setup-all-pdb (when you have one), and parameterize.it to generate the topology files.

./setup-no-pdb OHT
./parameterize.it OHT

Assuming drug name 'OHT'