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QuBe-SOMD_paper/FEP_preparation/01_Protein/README.md

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+- amberFF_files: Contains the pdb files of the proteins' fragments (for ligand groups 1 and 2) that can be parameterised with ff14SB
+- qube_files: Contains the xml/pdb files of the proteins' fragments (for ligand groups 1 and 2) that are paremetrised with QuBe along with instructions 
+on how to get the correstonding amber-type files for further processing with SOMD. 
+- xml_generation: Contains instructions for generating xml files from the protein pdb fragments in this study using QUBEKit-pro.

QuBe-SOMD_paper/FEP_preparation/01_Protein/amberFF_files/README.md

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+Both proteins of groups 1 and 2 consist of four fragments. 
+We need to parameterise each fragment separately and then combine them to form the proteins. 
+To parametrise the protein fragments with the ff14SB forcefield, we are using the [parameterise.py](https://github.com/michellab/BioSimSpace/blob/devel/nodes/playground/parameterise.py) script of BioSimSpace. 
+The script takes as an input the protein pdb file and returns the topology and coordinates amber files (prm7/rst7)
+
+- usage: run ./parameterise.py --input FILE.pdb --forcefield ff14SB --output amber_FILE
+
+To combine the newly parameterised fragments we use the [combine.py](https://github.com/michellab/BioSimSpace/blob/devel/nodes/playground/combine.py) script of BioSimSpace, that reads the amber files (2 moleculear systems at a time) 
+and combines them to form a complex. Then the coordinates and topology files of the complex are returned. 
+This process is done three times, in order to gradually construct the whole protein. 
+
+- usage: run ./combine.py --system1 amber_FILEx.prm7 amber_FILEx.rst7 --system2 amber_FILEy.prm7 amber_FILEy.rst7 --output amber_FILEx_y
+

QuBe-SOMD_paper/FEP_preparation/01_Protein/amberFF_files/group1/README.md

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+Coordinates files of the protein fragments (pdb) and amber files of the whole protein. **Need to add amber files?**

QuBe-SOMD_paper/FEP_preparation/01_Protein/amberFF_files/group2/README.md

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+Coordinates files of the protein fragments (pdb) for the protein used with the second group of ligands. 

QuBe-SOMD_paper/FEP_preparation/01_Protein/qube_files/README.md

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+To run FEP calculations with the QuBe forcefield, fisrtly we need to convert the protein files (xml/pdb) to amber type format(prm7/rst7).
+We use [qube_to_prmRst.py](https://github.com/cole-group/qube_project/blob/master/QuBe-SOMD_paper/FEP_preparation/qube_to_prmRst.py) to read the xml/pdb files of the protein fragments and generate the corresponding amber files:
+Usage: ~/sire.app/bin/ipython qube_to_prmRst.py -x fragX.xml -p fragX.pdb
+
+Then we combine the fragments to get the whole protein using [combine.py](https://github.com/cole-group/qube_project/blob/master/QuBe-SOMD_paper/FEP_preparation/combine.py).
+Usage: run ./combine.py --system1 fragX.prm7 fragX.rst7 --system2 fragY.prm7 fragY.rst7 --output fragX_Y
+
+Folders "Group1" and "Group2" contain the qube files (pdb/xml) of the protein fragments that can be used to generate the amber files for the proteins for the 
+respective set of ligands. 

QuBe-SOMD_paper/FEP_preparation/01_Protein/xml_generation/README.md

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+### Creating the files
+
+QUBEKit-pro is an extension to [QUBEKit](https://github.com/qubekit/QUBEKit) for analysing proteins.
+It comes bundled with the QUBEKit install and is accessed with the `QUBEKit-pro` command.
+
+Practically, creating the necessary files via QUBEKit is done simply through the command line interface. 
+Navigating to a directory containing the ONETEP output file and the relevant pdb files, the command 
+`QUBEKit-pro -build <name of pdb>` will perform the necessary steps described below.
+
+The requisite non-bonded parameter information is extracted from the ONETEP file. 
+QUBEKit-pro searches the ddec.onetep file top to bottom until all charge data is populated.
+As such, if using QUBEKit-pro for a fragment, 
+only the charge data for that fragment should be left in the ddec file (note that this process is not currently automated and users are responsible for generating and preparing the required ONETEP files).
+For each atom, this is the partial charge and the effective volume. 
+These parameters are then used to calculate the Lennard-Jones parameters via atom-in-molecule electron density partitioning. 
+Following this calculation, the atoms previously marked for symmetrisation are symmetrised. 
+These parameters are then stored for use in producing the final xml file.
+
+The files needed to reproduce the data in this paper are provided in the directory above.
+For example, in group1/frag2/ the input files are `frag2.pdb` and the (truncated) ONETEP output file corresponding to the atoms in fragment 2. The output files (`QUBE_pro_frag2.pdb` and `QUBE_pro_frag2.xml`) are generated using the command `QUBEKit-pro -build frag2.pdb`.
+
+
+Note that since each atom in the protein is in a unique environment, 
+and therefore has unique charge and Lennard-Jones parameters, 
+each atom in QUBEKit-pro is assigned a unique type. 
+This means the entire protein is to be treated as a single molecule rather than a collection of residues with fixed atom types.
+
+