Description:

mdms 1.0.4

MDMS: Molecular Dynamics Made Simple
Perform Molecular Dynamics (MD) Simulations from scratch within minutes. This program is an interface to one of the most popular MD codes (Amber), aiding users in preparing and running their own simulations.
The idea behind MDMS design is that the beginnings should be easy - not exhausting. That is why this program accommodates everything that is required for getting realistic insights about protein/protein-ligand complexes through MD simulations.
Program's execution has four distinct steps:

establishing protein/protein-ligand complex structure
preparing topology and coordinate files for Amber
preparing input files for Amber
running MD simulations

MDMS is aimed both to newcomers to the field as well as mature scientists. Newcomers will mostly benefit from the ease of starting MD simulations and the guarantee that the systems are constructed correctly (if user will carefully follow on-screen prompts). Mature scientists should mostly appreciate time savings - with MDMS, MD simulations of the proteins might be initiated as quickly as in 2 minutes from the start of the program.
Prerequisites

Linux distribution with Bash shell
Ambertools or Amber distribution
pdb-tools, biopython, numpy, pandas packages

Optional prerequisites

Openbabel distribution along with Pybel package
pdbfixer python package (part of Omnia software suite)
Propka3.1 python package

Installation
MDMS can be installed directly on your machine with either pip or conda.
Installing with pip:
pip install mdms
Installing with conda:
conda install -c szymonzaczek mdms
Installing dependencies
Depending on which installation you will use, not all of the dependancies might have been installed.
For instance, neither installations automatically install Amber Tools - it is assumed that you already have it on your machine (this is due to the fact that there are a lot of ways to customly install Amber Tools).
If you do not have required dependancies installed yet (and they were not installed along with MDMS installation), use conda or pip to download them:
conda install ambertools -c ambermd
pip install pdb-tools
pip install pandas
pip install numpy
pip install biopython
Optional dependancies
Following dependancies enable following functionalities:

Open Babel is used for adding hydrogen atoms to ligands
Propka is used to establish protonation states of residues within the structure
Pdbfixer program is used for modelling missing residues in proteins

They might be installed by running following commands in the console:
conda install -c openbabel openbabel
pip install PROPKA
conda install -c omnia pdbfixer
Getting Started
Change to the desired directory. All of the files will be stored there. Then simply type:
mdms_menu
Follow on-screen prompts to run your MD simulations!
Features

establishing initial protein (or protein-ligand complex) structure

downloading a protein structure directly from Protein Data Bank
using a protein structure that was earlier downloaded and/or somehow modified
choosing protein chains (if multiple chains are found in the structure)
checking if there are any missing atoms in amino acid residues
checking if there are any missing residues in the protein
adding missing residues with pdbfixer
reminding user that he should use functional oligomeric structure of the protein
establishing protonation states of titrable residues using Propka3.1
general formatting of PDB files
optional removal of residues, which are common leftovers after experiments
choosing which ligands are to be included for MD simulations
adding hydrogen atoms to ligands
choosing if metal ions are to be retained for MD (if they are present in the crystal structure)
choosing if crystal waters are to be retained for MD (if they are present in the crystal structure
adding hydrogen atoms to crystal waters


preparing topology and coordinate files for Amber

checking if there are hydrogen present in the ligand - if not, user is asked if this is on purpose
determining charges and force field parameters for ligands
processing chosen ligands and protein with pdb4amber
preparing input files for MCPB.py in order to obtain metal force field parameters
choosing protein force field
choosing water force field
choosing size of a solvation shell
creating topology and coordinate files


preparing input files for Amber

choosing routine for simulations (full simulations - minimization, heating, equilibration and production or only a single step-simulation)
choosing QM/MM parameters
option to provide premade QM/MM namelist file
choosing basic QM/MM parameters (QM atoms, spin, charge, QM Hamiltonian)
changing current and/or adding custom parameters
choosing MD parameters

default MD parameters for each step are provided
changing values of current MD parameters and the ability to add custom ones (though they must work with Amber codes)




running MD Simulations

choosing how simulations should be run - in queue or in terminal

if a queue was chosen, user must provide the appropriate script


choosing Amber code which will be run - Sander or PMEMD
choosing running mode - serial or parallel codes



Contributing
If you are interested in contributing to MDMS, please either contact me at szymon.zaczek@edu.p.lodz.pl or create pull request on Github.
License
MIT
Authors

Szymon Zaczek

License

For personal and professional use. You cannot resell or redistribute these repositories in their original state.

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