Qgui3

Gui for Q, The Molecular Dynamics Package

Qgui3 is a python3 package written by Geir Isaksen at the University of Tromso to ease the interaction and submission of jobs to the specialized Molecular Dynamics program Q. We say specialized as Q is tailored specifically to tackle the challenge of predicting accurate binding free energies, solvation free energies, and activation free energies since these are quantities of particular interest as they are the direct result of thermodynamic or kinetic experiments.

###Installation

Qgui is easy to install. The only demand on the user is that of making sure of having a working version of Q and Python3 (not installed using Conda) with the Tkinter, matplotlib, and numpy python packages used in the analysis modules.

If your installation of Python3 does not come with these packages, you can install them using:

bash-3.2$ apt-get install python3-tk
bash-3.2$ apt-get install python3-pip
bash-3.2$ pip3 install numpy
bash-3.2$ pip3 install matplotlib

Qgui3 can be cloned from github issuing the following command in the user terminal:

git clone https://github.com/qusers/qgui.git

This will ask for your github username and password.

As Qgui is written in python and uses its standard tkinter graphic libraries no more dependencies need to be fullfiled apart from installing the free for academics version of Maestro to be able to generate force-field libraries and parameters for ligand modeling. A working installation of pymol also comes handy for molecular visualization but it's not required.

Once downloaded the program can be invoked directly by typing the following command in the terminal:

bash-3.2$ python qgui.py

There is also an installation script to automatically set up Qgui on your MAC/LINUX. Simply run this by typing the following command in the terminal:

python3 INSTALL.py

or

./INSTALL.py

and follow the instructions given therin.

Alternatively, the user can also create an alias in their .cshrc or .bashrc file. For example for the case of .bashrc:

alias qgui="python /Users/username/software/qgui/qgui.py"

In the previous command you will have to replace username by your own and also give the correct path to where you have cloned Qgui.

###Examples The following are simple step-by-step examples of usage of Qgui from the ground-up.

####n-butane Now that you've installed Qgui and made sure that all additional packages are installed we can start with a simple example.

First you will have to create a PDB (Protein Data Bank) formatted coordinate file of n-butane, you can use pymol or avogadro, or download a coordinate file online and convert it to the correct format. A popular molecule repository is pubchem (https://pubchem.ncbi.nlm.nih.gov/). You can just go to pubchem and use the search box to query for n-butane scroll-down to the 3D-Conformer area and download the file in .sdf format. Later you can open the downloaded file in pymol and save the file as .pdb. You will still have to do some editing and delete all rows starting with CONNECT and replace HETATM with ATOM making sure to include two spaces to replace the T, and M, letters in HETATM. Finally you will have to replace UNK with LIG. Now you finally have a clean file you can work with.

Next step is to go ahead and fire-up Qgui from a terminal with your brand new alias:

qgui

Now you will have to make sure that the settings point to the right places. In the upper side of your screen go to File/Settings and make sure that the name of the executables for Q correspond to the ones in your system (e.g. qprep5, qdyn5). Also set-up the path to the schrodinger installation, usually it is automatically installed at:

/opt/schrodinger/suites2014-1

Also add the path to the oplsaa parameter and library files and finally click on save.

As you will also want to have all files in the same folder holding your n-butane.pdb file go to File/Change workdir and make sure to select the folder holding your n-butane pdb file.

Now you can proceed to load your PDB file by clicking on Load, and Browse to the folder where your file is located.

Once loaded you will want to generate parameters for you ligand. Go to Prepare/Parameters, select the atoms in your pdb file and select a force-field. Then click on Run. If succesful a new window will pop-up telling you that a library file with a corresponding pdb, and parameter file has been generated.

Now go back to File/Setttings and load the LIG.lib library file and the QOPLS2001_LIG.prm parameter file which have just been generated. Qgui takes care of assembling a new parameter file which merges the oplsaa parameters and the newly generated ligand parameters into a new file called merged.prm. You must always check that file to make sure that the parameter assignment makes chemical sense.

Now you can generate a topology file. Go to Prepare/Topology, make sure all options are as you want them, for example, TIP3 water model or SPC, etc. Click on Run to launch Qprep, or Write if you just want to write the input files.

Now you are ready to run simulations.

To run an MD simulation just go to Setup/MD and look at the options with care. At this step if you have an experienced Q user close by it would be useful so that someone can aid on understanding the meaning of the options provided in the Setup MD window, of course, you can always turn to the Q users manual.

After making sure that you've set-up the option most appropiate for your simulation you can click on Run, and, if no error messages pop-up, wait for approximately 10 minutes running the non-parallel version of qdyn5 on a 3.3GHz intel core i7 processor with 16Gb of RAM. Alternatively, you can press Write to write the files to disk, and submit them from command line.

The analysis tools in Qgui are quite powerful and customizable as they rely on the matplotlib and numpy python libraries. Usage examples of the analysis tools will soon be explored here.