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respyte

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Implementation of open-source version of RESP method

New version of respyte can be found in re-formatting branch:) Will be merged to master soon!

Installation

From a clean Miniconda installation, run the following:

conda create --name respyte python=3.6
source activate respyte
conda install -c psi4 psi4
conda install -c openeye openeye-toolkits
conda install pandas scipy pyyaml matplotlib future
conda install -c conda-forge pymbar
conda install -c omnia forcebalance

and run setup.py for installation:

python setup.py install

Running

Before running 'esp_generator.py', Please navigate 'data' folder which contains sample input folder. This will give you some idea about what kind of data structure 'esp_generator.py' and 'resp_optimizer.py' can handle.

First, to calculate electrostatic potential (and electric field) using Psi4, create input folder with appropriate data structure and run this command inside the directory where your input/ folder exists:

respyte-esp_generator

If the calculation is successfully done, you can find files with .espf extension in each subfolder,'input/molecules/mol(i)/conf(j)'. This stores all the grid point informations with specific file format for 'resp_optimizer.py'. Then you are ready to go to the next step. Write respyte.yml inside <input-dir-name> and run this command where your <input-dir-name> folder exists:

respyte-optimizer input-dir-name

Copyright

Copyright (c) 2018, Hyesu Jang

Acknowledgements

Project based on the Computational Molecular Science Python Cookiecutter

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