Merge pull request #7 from libefp2/new_jack

fixing my conflicting files

Author: Jacklaw441

applied_efp.rst

@@ -0,0 +1,105 @@
+.. _FlexEFP_fmo.rst:
+
+*************************
+FMO: Applied flexible EFP
+*************************
+
+Overview
+--------
+
+As is the case with many photoactive proteins,computational methods struggle to reproduce 
+experimental spectra for the Fenna-Matthews-Olson complex (FMO). Work by 
+`Kim et al <https://pubs.acs.org/doi/full/10.1021/acs.jpclett.9b03486>`_ shows that 
+flexible QM/EFP can be applied to FMO to correctly generate computational results in 
+quantitative agreement to experimental spectra. 
+
+The key to applying EFP to your system is to carefully define the active site and EFP region. 
+FMO is a trimeric protein with eight bacteriochloropyll a (BChl) pigments in each monomer. 
+FMO completes energy transfer via excitonic couplings across these eight BChls. A summary 
+of the complete workflow that was performed is the following: 1) molecular dynamics (MD) 
+simiulations of the FMO protein in water and counter ions, 2) QM/MM (not EFP) geometry 
+optimization of *each* active site (active sites consist of one BChl pigment and 
+typically 3 H-bonding amino acids), and 3) flex-EFP excited state energy calculations of 
+each pigment.
+
+In the case of FMO, these steps must be repeated on several snapshots from MD to account 
+for variation in the resting state of the structure, and the QM region must be defined 
+carefully in both the QM/MM and flex-EFP stages. It might not be universally true that one 
+must perform QM/MM geometry optimization. This page is a walkthrough for the flex-EFP procedure 
+only. Molecular dynamics and QM/MM optimizations are assumed to be complete for your 
+system prior to these steps. 
+
+.. image:: images/FMO_trimer_BCLs.bmp
+   :width: 350
+   
+.. image:: images/FMO_mon_pigs.bmp
+   :width: 400
+
+You will need a structure file (.g96) and topology information (.top, for atom charges). In this specific case,
+a structure file is extracted from a GROMACS molecular dynamics trajectory and all water molecules more than 15 angstroms from 
+the protein's surface have been removed. For a chlorophyll-containing protein, you will likely want to optimize the geometry 
+of each active chlorophyl molecule (with very close amino acids/water molecules) separately with more standard QM/MM approaches 
+before proceeding with EFP calculations on the optimized geometry. For this example, the first BChl, residue number 359, 
+has been optimized and will be the QM region for the EFP calcuation.
+
+.. image:: images/fmo_waters15a.bmp
+   :width: 400
+
+First, an EFP region must be defined. Every amino acid, (non QM) BChl, and water molecule containing an 
+atom within 15 angstroms of the QM BChl headring. 
+
+The headring is defined by atomnames: MG CHA CHB HB CHC HC CHD HD NA C1A 
+C2A H2A C3A H3A C4A CMA HMA1 HMA2 HMA3 NB C1B C2B C3B C4B CMB HMB1 HMB2 HMB3 CAB OBB CBB HBB1 HBB2 HBB3 NC C1C C2C H2C C3C 
+H3C C4C CMC HMC1 HMC2 HMC3 CAC HAC1 HAC2 CBC HBC1 HBC2 HBC3 ND C1D C2D C3D C4D CMD HMD1 HMD2 HMD3 CAD OBD CBD HBD CGD O1D O2D 
+CED HED1 HED2 HED3
+
+The headring surrounded by EFP region looks like this:
+
+.. image:: images/tester.bmp
+   :width: 400
+
+EFP is, of course, a fragmentation method. The protein residues within the 15 angstrom cutoff will be expressed individually. 
+Because amino acids are a continuous chain, we will need to break each residue into its own fragment. Chemically, we would like 
+to divide each residue by the C-C backbone bond, however, standard PDB listing convention divides residues by the C-N 
+bond. To correct this, 'C' and 'O' atom names should be included in the following aminoc acid. This way the 'C' and 'CA' 
+(carbonyl carbon and alpha carbon respectively) bond is the division between bonded fragments.
+See the example below:
+
+.. image:: images/pdb_67_col.bmp
+   :width: 400
+
+For EFP, we would like these two fragments to look like this:
+
+.. image:: images/efp_67_col.bmp
+   :width: 400
+
+The desired atoms are contained in the structure file, but they do not completely 'agree' with the amino acid numbering.
+Below is a snippet from the structure file with the desired EFP fragment 8 highlighted. Note that atom names 'C' and 'O' 
+have to be included in the following fragment.
+
+.. literalinclude:: ./examples/flex-EFP/1.Prepare_Structure/bchl359-50028.g96
+   :linenos:
+   :lines: 79-101
+   :emphasize-lines: 10-21
+
+Next, the BChl molecules are closer than the 15 angstrom cutoff, so they also appear in the EFP region. It is more cost efficient 
+to treat BChl fragments as separate head and tail groups as is shown below:
+
+.. images/efp_headtail.bmp
+   :width: 400
+   
+In the case of both amino acid and BChl fragments, we have at least one broken bond; we cannot simply compute a fragment that is 
+missing an atomic bond. To solve this, we will introduce virtual hydrogen atoms to 'cap' the broken bonds. Non terminal 
+amino acid fragments will have two virtual atoms. The first is between the alpha carbon of the previous residue and the 
+carbonyl carbon of the current residue; the other is similarly between the alpha carbon of the current residue and the carbonyl carbon 
+of the following residue. The BChl fragments are split between atoms 'C2A' and 'CAA.' One virtual atom will be added to both 
+head and tail fragments between these atoms. Virtual atoms are added along the vector of the broken bonds with the distance changed 
+to the C-H equilibrium bond distance, 1.09 angstroms.
+
+.. images/efp_bothvirt.bmp
+
+Once the system is properly fragmented, we can finally run EFP calculations in the precense of the polarizable, solvatochromic environment. 
+
+EFP Workflow
+------------
+