diff --git a/README.md b/README.md index 5560eaf6..900d8ae2 100644 --- a/README.md +++ b/README.md @@ -61,24 +61,24 @@ the address displayed in the console window (e.g. http://127.0.0.1:5000). Download the processed PDB file and Python script, which will serve as input for the **OpenMMDL Simulation** script. -## OpenMMDL-Simulation +## OpenMMDL Simulation -OpenMMDL-Simulation starts the MD simulation with the inputs acquired -from OpenMMDL-Setup +**OpenMMDL Simulation** starts the MD simulation with the inputs acquired +from **OpenMMDL Setup**. ### Usage Start the simulation with the following Inputs: #### Mandatory: --f = name of the folder, where the MD simulation files are stored +-f = Name of the folder, where the MD simulation files are stored -t = Topology file of your protein from the setup including the path -s = Python script from the setup including the path #### Optional: --l = SDF File of the ligand, if the ligand was selected during the +-l = SDF file of the ligand, if the ligand was selected during OpenMMDL Setup. The SDF file name should be consistent with the input in the setup -c = Coordinates file of Amber @@ -88,12 +88,12 @@ Setup. The SDF file name should be consistent with the input in the setup openmmdl_simulation -f {path/to/folder_name} -t {path/to/topology} -s {path/to/script} -l {path/to/ligand} -## OpenMMDL-Analysis +## OpenMMDL Analysis -OpenMMDL-Analysis performs an analysis of the MD simulation obtained from OpenMMDL-Simulation. +**OpenMMDL Analysis** performs an analysis of the MD simulation obtained from **OpenMMDL Simulation**. It analyzes the protein-ligand complex interactions throughout the MD trajectory, delivering the list of -all possible interactions. In addition, it generates interaction fingerprints, provides the most occurring binding modes -, and displays the transitions between the separate binding modes. +all possible interactions. In addition, it generates interaction fingerprints, provides the most occurring so called Binding Modes +and displays the transitions between the separate binding modes. If there is no ligand given, OpenMMDL-Analysis will instead analyze the trajectory on stable watermolecules and cluster those at positions where in at least 75% of the MD a watermolecule is present. Outputs include a PDB with representative waters @@ -105,32 +105,34 @@ and a CSV of nearby protein Residuenumbers and chains as well as PDBs of each wa Start the analysis with the following Inputs: #### Mandatory: --t = Topology file (PDB) - --d = Trajectory file (DCD) - --l = SDF File of the ligand - --n = Name of the ligand in the PDB file +-t = topology file of the simulation (in .pdb format) +-d = trajectory file of the simulation (in .dcd format) #### Optional: --b = Binding mode treshold, which is used to remove interactions under a certain procentual occurence treshold from the binding mode generation, default is 40 (values: 0-100) - --df = Dataframe File, if all of the interaction already were calculated. The default name of this file, which is obtained after calculating the interactions is interactions_gathered.csv - --m = Minimal Transition, which is a treshold applied for the display of the binding mode transitions via a markov chains network figure, the defaul value is 1. - --c = CPU count, which will be used to calculate interactions. The default value is half of the CPU count. +-n = Ligand name (3 letter code in PDB) +-l = Ligand in SDF format +-b = binding mode threshold. Is used to remove interactions under the defined procentual occurence from the binding mode generation. The default is 40% (accepted values: 0-100) +-df = Dataframe (use if the interactions were already calculated, default name would be "interactions_gathered.csv") +-m = minimal transition threshold. Is used for the display of the binding mode transitions in the Markov state chains network figure. The default value is 1 +-c = CPU count, specify how many CPUs should be used, default is half of the CPU count. +-p = Generate .pml files for pharmacophore visualization. The default is False (accepted values: True/False) +-s = special ligand name to calculate interactions with special ligands. +-nuc = Treat nucleic acids as receptor +-pep = Calculate interactions with peptides. Give the peptide chain name as input. Defaults to None +-ref = Add a reference PDB to renumber the residue numbers. Defaults to None (accepted values: str of PDB) +-r = Calculate the RMSD difference between frames. The default is False (accepted values: True/False) +-w = stable-water-analysis. Defines if the analysis of stable water molecules should be performed. The default is False (accepted values: True/False) +--watereps = the EPS of the clustering part during the water analysis. will only result in something if "-w True" is added. Accepts float (in Angstrom). #### Command line example with default values - openmmdl_analysis -t {path/to/topology} -d {path/to/trajectory} -l {path/to/sdf_ligand} -n {Ligand_name} + openmmdl_analysis -t {path/to/topology} -d {path/to/trajectory} -n {Ligand_name} #### Visualization Most of the analysis outputs are JEPG images and do not need any further preparation to be viewed. -For the visualization of your trajectory with interaction pointclouds you can use the jupyter notebook prepared in the OpenMMDL repository. +For the visualization of your trajectory with interaction pointclouds you can use the jupyter notebook prepared in the **OpenMMDL** repository. Or use this command: ```