vahtras/moltools

Polarizable QMMM force field development for proteins.

#Welcome to moltools!

Code purpose: Wrap DALTON LoProp calculation into convinient functions
callable by the Molecule instance using IPython or python scripts.

Current features:

Features include obtaining LoProp properties for solvent molecules/ligands 
or for proteins and polymers that are covalently bonded via the MFCC procedure.

By integrating with the particles module, applequist equations are directly 
solvable for a system of classical molecules using damped 
charges/dipole-moments 	directly from QM-obtainable properties.

For localized Beta, this requires the latest development source of 
DALTON installed.

Installation:

git clone --recursive [email protected]:fishstamp82/moltools.git

export PYTHONPATH=$(pwd)/moltools/src:$PYTHONPATH

Tip: Export the pythonpath variable in your initrc file of choice in order to have it automatically load.

Execute the following script if you want to run DALTON computations in parallel using HPC clusters.

For the Linköping HPC triolith, execute:

src/scripts/dalton_run_on_triolith.sh

For Umeå HPC akka, execute:

src/scripts/dalton_run_on_akka.sh

A quick-start:

Run:

• ipython
• in [1]: from molecules import Water, Cluster

Create a water molecule with oxygen in origo, in atomic units by default

in [2]: w1 = Water().get_standard()

Create an additional water molecule (atomic units by default)

in [3]: w2 = Water.get_standard()

Translate water 2 by 2.5 AU in the z-axis

in [4]: w2.translate_by_r( [0, 0, 2.5] )

Add them together into a Cluster

in [5]: c = Cluster( w1, w2 )

You can always make a quick visualization of a Molecule / Cluster

in [6]: c.plot()

Attach some properties to the waters (The rotation of properties will be taken care of )

#See template.py for all available templates

in [8]: c.attach_properties( model = 'tip3p', method = 'HF', basis ='ANOPVDZ' )

Output the atomic/ molecular/ cluster propertiy via the .Property keyword, or via the quick-wrapper .p (.d for dipole, .a alpha .etc )

in [9]: print c.p.a [ 15.02184 0. 0. 11.48016 0. 13.72182]

Calculate each waters properties from ab-initio using DALTON, and put those properties on each atom using LoProp in one step:

In [10]: c.props_from_qm( tmpdir = '/tmp', dalpath = $PATH_TO_DALTON_SCRIPT )

If the dalton version is the development master branch, localized hyperpolarizabilities are obtainable:

In [11]: c.props_from_qm( method = 'b3lypqua', tmpdir = '/tmp', dalpath = $PATH_TO_DALTON_SCRIPT )

---

Extra features:

These include uncommenting "#from mayavi import mlab" in 
src/pdbreader.py and an installation of mayavi2.
This enables plotting of the beta tensor around molecules and clusters.

######Visit the documentation for the API and more tutorials on the source code. Work in progress and most stuff are outdated.