update of applied_efp tutorial

Author: slipchenko

.DS_Store

@@ -1,16 +1,18 @@
 .. _bioefp:
 
-******
-BioEFP
-******
+**********************************
+BioEFP - extending EFP to proteins
+**********************************
 
 BioEFP is a scheme to split a macromolecule into fragments.
 Proteins can be split along C-Ca bonds, as shown below.
 
 .. image:: ../images/BioEFP.jpg
-   :width: 200
+   :width: 400
 
 The model is described `here <https://pubs.acs.org/doi/abs/10.1021/acs.jpcb.6b04166>`_.
-The original work used the following script `step2.gen.gamess.pl` **Where is it?**.
-For a new robust version of the script check out this
-`BioEFP tutorial <https://github.itap.purdue.edu/Slipchenko-group/>`_ **The tutorial is not there yet!**
+
+Check out our tools and tutorials on how to
+
+* prepare a protein system for `EFP protein-ligand calculations <https://github.com/libefp2/BioEFP-tools/tree/main/bioMAKEFP>`_
+* prepare a protein system for QM/EFP calculations :ref:`applied_efp`

doc/.DS_Store

@@ -30,12 +30,12 @@
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-#extensions = [
-#    'sphinx.ext.autosectionlabel', 'sphinx_rtd_theme',
-#]
 extensions = [
-    'sphinx.ext.autosectionlabel', 'sphinx_rtd_theme', 'sphinx_panels',
+    'sphinx.ext.autosectionlabel', 'sphinx_rtd_theme',
 ]
+#extensions = [
+#    'sphinx.ext.autosectionlabel', 'sphinx_rtd_theme', 'sphinx_panels',
+#]
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']

doc/applied_efp.rst

@@ -1,11 +1,15 @@
 .. _flexible_efp:
 
-******
+************
 Flexible EFP
-******
+************
 
 But wait, do I need to recompute fragment parameters for each new geometry of my
 polymer? Not necessary, if you did a homework. Check out this paper on
 `Flexible EFP <https://pubs.acs.org/doi/abs/10.1021/acs.jpcb.6b04166>`_.
-A collection of scripts to help you set-up these jobs
-is `Flexible EFP tutorial <https://github.itap.purdue.edu/Slipchenko-group/Flexible_EFP_scripts/>`_.
+
+The original code developed by Dr. Yongbin Kim can be found
+`here <https://github.com/libefp2/libefp/blob/master/tools/Flexible_V5.py>`_.
+
+Check out our tutorial showing how to setup QM/EFP calculations for a protein
+system using Flexible EFP procedure! :ref:`applied_efp`

doc/bioefp.rst

@@ -28,7 +28,6 @@ EFP, or the Effective Fragment Potential, is a polarizable quantum-mechanics-bas
    efp_calcs
    bioefp
    flexible_efp
-   applied efp
    qmefp
 
 

doc/conf.py

@@ -17,13 +17,13 @@ Review papers
 * `2013 review of EFP2 developments <http://dx.doi.org/10.1146/annurev-physchem-040412-110031>`_
 * `2011 review of fragmentation models <http://dx.doi.org/10.1021/cr200093j>`_
 * `2014 FMO v/s EFP v/s EFMO <https://doi.org/10.1021/ar500097m>`_
- 
+
 Book chapters
 ^^^^^^^^^^^^^^^^
 * `2007 The Effective Fragment Potential: A General Method for Predicting Intermolecular Interactions <https://doi.org/10.1016/S1574-1400(07)03010-1>`_
 * `2017 Effective Fragment Potential Method: Past, Present, and Future <https://doi.org/10.1002/9781119129271.ch6>`_
 
-Software and model development 
+Software and model development
 -------------------------------
 
 Development of EFP terms
@@ -80,8 +80,8 @@ Intermolecular interactions
 * `Interactions Between Halide Anions and a Molecular Hydrophobic Interface <http://dx.doi.org/10.1039/C2FD20082A>`_
 * `Interactions between Noble Metal (Ag and Au) Nanoclusters and Water using EFP <https://doi.org/10.1021/acsomega.0c00132>`_
 * `Unusual symmetry of hexafluoro-o-xylene <https://doi.org/10.1063/1.5142169>`_
-  
-* `Quantifying the Nearly Random Microheterogeneity of Aqueous tert-Butyl 
+
+* `Quantifying the Nearly Random Microheterogeneity of Aqueous tert-Butyl
   Alcohol Solutions Using Vibrational Spectroscopy <https://doi.org/10.1021/acs.jpclett.3c02603>`_
 
 Electronic excited states and properties
@@ -92,21 +92,23 @@ Electronic excited states and properties
 * `Ionization potentials of hydrated thymine <http://dx.doi.org/10.1021/jp110438c>`_
 * `Solvatochromic shifts in p-nitroaniline <http://dx.doi.org/10.1021/jp110026c>`_
 
-* `The effect of polarizable environment on two-photon absorption cross sections characterized 
-  by the equation-of-motion coupled-cluster singles and doubles method combined with the 
+* `The effect of polarizable environment on two-photon absorption cross sections characterized
+  by the equation-of-motion coupled-cluster singles and doubles method combined with the
   effective fragment potential approach  <https://doi.org/10.1063/1.5048627>`_
 
 * `EFP for simulation of excited states in an inhomogeneous environment <https://doi.org/10.1002/qua.26071>`_
 * `EFP for Microsolvated Excited and Anionic States <https://dx.doi.org/10.1021/acs.jpca.2c06122>`_
 
-* `Coupled-cluster based approach for core-level states in condensed phase: Theory and 
+* `Coupled-cluster based approach for core-level states in condensed phase: Theory and
   application to different protonated forms of aqueous glycine <https://dx.doi.org/10.1063/1.4990564>`_
 
+.. _bio_papers:
+
 Biological chromophores
 ^^^^^^^^^^^^^^^^^^^^^^^^^
 
 * `Predictive First-Principles Modeling of a Photosynthetic Antenna Protein: The Fenna-Matthews-Olson Complex <https://doi.org/10.1021/acs.jpclett.9b03486>`_
-* `Predicting Mutation-Induced Changes in the Electronic Properties of Photosynthetic 
+* `Predicting Mutation-Induced Changes in the Electronic Properties of Photosynthetic
   Proteins from First Principles: The Fenna-Matthews-Olson Complex Example <https://doi.org/10.1021/acs.jpclett.3c01461>`_
 
-* `Polarizable embedding for simulating redox potentials of biomolecules <http://dx.doi.org/10.1039/C9CP01533G>`_
+* `Polarizable embedding for simulating redox potentials of biomolecules <http://dx.doi.org/10.1039/C9CP01533G>`_

doc/flexible_efp.rst

@@ -37,6 +37,8 @@ An example of GAMESS input file for computing EFP parameters :download:`makefp.i
 .. literalinclude:: ../examples/makefp.inp
   :linenos:
 
+.. _efp parameters:
+
 `.efp` parameter file
 ----------------------
 
@@ -386,7 +388,7 @@ Some wisdom on a choice of the POLAB parameter:
 - The section ends with mandatory ``STOP`` line.
 - GROMACS units are assumed: :math:`\sigma` in nm, :math:`\epsilon` in kJ/mol.
 
-Currently, the Lennard-Jones energy is computed as 
+Currently, the Lennard-Jones energy is computed as
 
 .. math::
 
@@ -395,12 +397,12 @@ Currently, the Lennard-Jones energy is computed as
 using the following comboination rules
 
 .. math::
-  
+
   \sigma_{ij} = 0.5 * (\sigma_i + \sigma_j)
-  
+
   \epsilon_{ij} = \sqrt{\epsilon_i * \epsilon_j}
 
 .. literalinclude:: ../examples/tip3p_mm.efp
   :linenos:
   :lines: 73-82
-  :emphasize-lines: 1, 6
+  :emphasize-lines: 1, 6

doc/index.rst

@@ -4,6 +4,7 @@
 QM/EFP
 ******
 
-QM/EFP are powerfull and efficient methods to analyze solute-solvent interactions and electronic properties in condensed phases. Implementations in GAMESS, Q-Chem, and PSI4 have been developed.
+QM/EFP are powerfull and efficient methods to analyze solute-solvent interactions and electronic properties
+in condensed phases. Implementations in GAMESS, Q-Chem, and PSI4 have been developed.
 
 Formulas...