ChemFlow
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IFMlab
Computational Chemistry Workflows
Ligand preparation (PDBQT) do not work with other version of MGLTools than 1.5.6. tested 1.5.4 and 1.57 Also MGLtools is not listed in the required softwares
Enable GBSA models igb=1,2,5,8 Implement PBSA (igb=RTFM) Most GB/PB model parameters are auto-assigned during runtime (AMBER) for Minimization and MD simulations after "igb" is defined. For MM(PB,GB)SA post-processing it is...
python SmilesTo3D.py -i test.smi Fatal Python error: PyThreadState_Get: no current thread Abort trap: 6 It's a know issue. https://github.com/rdkit/rdkit/issues/1617
LigFlow/ScoreFlow should first search for a compound in ChemBase for parameters instead of recomputing all over again. This is especially important for am1-bcc and even more for RESP which take...
I just realized that antechamber can not be executed at the concurrently at the same folder. For each ligand it generates a number of temporary files with the same name...
MMGBSA needs "ante-MMPBSA.py" to generate the input files, It takes some time because it's a python script, and could be easly done in parallel. In addition, post-processing MD simulations of...
During --postdock a user may select, the final result will be a filtered. Possible add an --output_mol2 and --output_csv file .mol2 and .csv after filters. 1. Number of poses /...
1. Choice of implicit model: igb=2,5,8 for GBSA igb=1,3 for PBSA. 2. Choice of interval: Default 10. Input file for running GB2 &general verbose=0,keep_files=0,interval=${INTERVAL} / &gb igb=${IGB}, saltcon=0.150 /