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EasyHybrid, a QM/MM interface for PyMOL

已有 3047 次阅读 2017-3-15 02:02 |系统分类:科研笔记



The QM/MM calculation is very tedious because of difficulties in defining QM/MM region. EasyHybrid - GTKDynamo is free/open source software which, together with pDynamo, transforms PyMOL into a powerful interface for molecular modeling. The interface has been designed to facilitate determining reaction pathways in biological systems, specially using hybrid QC/MM (or QM/MM) methods. Pymol has been chosen as a graphical interface to pDynamo because it has a python API with wide documentation available. EasyHybrid use ORCA, which can be otained for free from here,  as the QM/MM engin in the backend.

Some of the pDynamo capabilities that can be used with the EasyHybrid:

· Pure QC simulations - ab initio and SMO.

· Pure MM simulations - using AMBER, CHARMM or OPLS force fields.

· Hybrid QCMM simulations.

· Single point calculations.

· Energy minimization.

· Molecular dynamics.

· Reaction coordinate scanning.

· Umbrella sampling.

· Reaction path calculations - using NEB.

· and more...

Download link:

https://sites.google.com/site/gtkdynamo/download

Citation:

J. F. R. Bachega, L. F. S. M. Timmers, L. Assirati, L. B. Bachega, M. J. Field, T. Wymore. J. Comput. Chem. 2013, 34, 2190-2196. DOI: 10.1002/jcc.23346

Installation

EasyHybrid is available for download for linux and Mac platforms. The installation process is simple, once you have downloaded the program, unpack the file typing:


..$ tar -xzvf EasyHybrid_verX.X.tar.gz     or    ..$ unzip gtkdynamo2-master.zip


and execute the installation script file:


..$ cd EasyHybrid_verX.X                   or    ..$ cd gtkdynamo2-master

../EasyHybrid_verX.X$ python install.py    or    ../
gtkdynamo2-master$ python install.py


The script will verify if your system has all external packages automatically, you just need to accept the installation. The first step, you will be argued about your operational system:


       Operational system:

           (1) Ubuntu / Debian / Mint            (apt-get)

           (2) Fedora                            (dnf)

           (3) Suse   / OpenSuse                 (zypper)

           (4) Gentoo                            (emerge)

           (5) MacOS                             (port)

           (6) CentOS                            (yum)

           (0) Other                             (Do it by yourself...)        

Please, choose the OS by the number(1):

Note: if you are using MacOS, make sure that you have also installed the Xcode (https://guide.macports.org/chunked/installing.xcode.html) and Macports (https://www.macports.org/), since the installation script will use "port" to install all external packages.


Since you have specify the operational system, the installation script will check all external packages and, if necessary, the missing packages will be installed.


Checking dependencies

gtk..............................OK

pygtk............................OK

PyMOL............................OK

matplotlib.......................OK


Checking pDynamo

pBabel...........................OK

pCore............................OK

pMolecule........................OK

pMoleculeScripts.................OK


After proper installation, the following messages are expected:


- - - Installation successful - - -



       "Happy simulating :)"

Note: If you are using CSH, you need to setup the environment variable manually.


Installation complete. To run Easyhybrid just type "easyhybrid" in your terminal.


..$ easyhybrid


Tips: EasyHybrid has been tested in many different desktop environments. We recommend: Xfce, Gnome2 (gnome classic), and openBox.


tcsh or csh environment can be configurated manually:






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