ChemFlow
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IFMlab
Computational Chemistry Workflows
I suggest to start by AMBER parameters. 1. ChemFlow --write-config to write a configuration file. 2. Something like ChemFlow --config **project_protocol_target_chemflow.config** should be enough to run. 3. Include ALL mandatory...
There are multiple flavors for MM-(GB)SA, one should be abble to access at least some of the parameters within ScoreFlow during simulation. 1) Choice of simulation engine: AMBER serial: sander...
Implement selections for DockFlow output using --postdock. The actions currently in "ChemFlow_tools.bash" and allow the user to select and output: * ALL compounds, ranked by energy + ALL docking poses...
Dear ChemFlow developers, we should not forget to put a header (when running the code) indicating our affiliation (University of Strasbourg), link to the IFM website, relevant publications and the...
What's a scoring function, how different can they be for docking, virtual screening and rescoring. What else can use (that actually works) to rank docking poses ?
I must incorporate it to ChemFlow but 1st must addequate it to the .config format
As mentioned by Simone some time ago, in due time we will need to check with the University which licence should be used.
Currently Tripos mol2 it the default input format for both receptor and ligand in DockFlow and ScoreFlow, and for compounds in LigFlow. RDKit does not write a .mol2 file, sticking...
File Input/Output is not an issue with small libraries with hundreds of files and local SSD disks. But when we move to a cluster/supercomputer like mesocentre that becomes an important...
We will close modifications to DockFlow & ScoreFlow by end of July. We must preserve Tools, MDFlow and HGFlow originals and merge the rest.