Package: mdms
MDMS: Molecular Dynamics Made SimplePerform 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 structurepreparing topology and coordinate files for Amberpreparing input files for Amberrunning MD simulationsMDMS 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.PrerequisitesLinux distribution with Bash shellAmbertools or Amber distributionpdb-tools, biopython, numpy, pandas packagesOptional prerequisitesOpenbabel distribution along with Pybel packagepdbfixer python package (part of Omnia software suite)Propka3.1 python packageInstallationMDMS can be installed directly on your machine with either pip or conda.Installing with pip:pip install mdmsInstalling with conda:conda install -c szymonzaczek mdmsInstalling dependenciesDepending 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 ambermdpip install pdb-toolspip install pandaspip install numpypip install biopythonOptional dependanciesFollowing dependancies enable following functionalities:Open Babel is used for adding hydrogen atoms to ligandsPropka is used to establish protonation states of residues within the structurePdbfixer program is used for modelling missing residues in proteinsThey might be installed by running following commands in the console:conda install -c openbabel openbabelpip install PROPKAconda install -c omnia pdbfixerGetting StartedChange to the desired directory. All of the files will be stored there. Then simply type:mdms_menuFollow on-screen prompts to run your MD simulations!Featuresestablishing initial protein (or protein-ligand complex) structuredownloading a protein structure directly from Protein Data Bankusing a protein structure that was earlier downloaded and/or somehow modifiedchoosing protein chains (if multiple chains are found in the structure)checking if there are any missing atoms in amino acid residueschecking if there are any missing residues in the proteinadding missing residues with pdbfixerreminding user that he should use functional oligomeric structure of the proteinestablishing protonation states of titrable residues using Propka3.1general formatting of PDB filesoptional removal of residues, which are common leftovers after experimentschoosing which ligands are to be included for MD simulationsadding hydrogen atoms to ligandschoosing 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 structureadding hydrogen atoms to crystal waterspreparing topology and coordinate files for Amberchecking if there are hydrogen present in the ligand - if not, user is asked if this is on purposedetermining charges and force field parameters for ligandsprocessing chosen ligands and protein with pdb4amberpreparing input files for MCPB.py in order to obtain metal force field parameterschoosing protein force fieldchoosing water force fieldchoosing size of a solvation shellcreating topology and coordinate filespreparing input files for Amberchoosing routine for simulations (full simulations - minimization, heating, equilibration and production or only a single step-simulation)choosing QM/MM parametersoption to provide premade QM/MM namelist filechoosing basic QM/MM parameters (QM atoms, spin, charge, QM Hamiltonian)changing current and/or adding custom parameterschoosing MD parametersdefault MD parameters for each step are providedchanging values of current MD parameters and the ability to add custom ones (though they must work with Amber codes)running MD Simulationschoosing how simulations should be run - in queue or in terminalif a queue was chosen, user must provide the appropriate scriptchoosing Amber code which will be run - Sander or PMEMDchoosing running mode - serial or parallel codesContributingIf you are interested in contributing to MDMS, please either contact me atszymon.zaczek@edu.p.lodz.plor create pull request on Github.LicenseMITAuthorsSzymon Zaczek