Problem in generation of some map files during flexible autodock docking.

[aditya-jugade]

For my ligands HD Map file is not generating but other required map file are generating for ligands. Can you please tell me how to resolve this, as during docking HD map files required.

[rwxayheee]

Hi @aditya-jugade
A similar issue was reported in #312 would any of you be able to share your input files and commands? We can check your inputs, try to reproduce and follow up with you

[aditya-jugade]

/path/pythonsh prepare_flexreceptor.py -r 7MYI.pdbqt -s ASP228_ASP32_TYR71_PHE108_SER35 -g 7MYI_receptor_rigid.pdbqt -x 7MYI_receptor_flex.pdbqt
/path/mgltools_x86_64Linux2_1.5.7/bin/pythonsh /path/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_gpf4.py -l ligand -r 7MYI_receptor_rigid.pdbqt -y
/path/autogrid4 -p 7MYI_receptor_rigid.gpf -l 7MYI_receptor_rigid.glg

above is the command to generate map file, input is pdbqt files for both receptor and ligand.
7MYI.txt
1PY1.txt
1PY1 is one of the ligand file
7MYI is receptor file.
I have attached both the file as txt as github is not supporting pdbqt format but original files are in pdbqt format only.
cmd is running but unable to generate HD files for ligands

[rwxayheee]

Hi @aditya-jugade
Thanks for the info! The problem is likely because of step 2
/path/mgltools_x86_64Linux2_1.5.7/bin/pythonsh /path/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_gpf4.py -l ligand -r 7MYI_receptor_rigid.pdbqt -y
produces a GPF file 7MYI_receptor_rigid.gpf with

npts 40 40 40                        # num.grid points in xyz
gridfld 7MYI_receptor_rigid.maps.fld # grid_data_file
spacing 0.375                        # spacing(A)
receptor_types A C OA N SA HD        # receptor atom types
ligand_types A P C OA N              # ligand atom types

Please consider adding the option to specify flexible residues, like the following:
pythonsh prepare_gpf4.py -l ligand -r 7MYI_receptor_rigid.pdbqt -x 7MYI_receptor_flex.pdbqt -y
will give you

npts 40 40 40                        # num.grid points in xyz
gridfld 7MYI_receptor_rigid.maps.fld # grid_data_file
spacing 0.375                        # spacing(A)
receptor_types A C OA N SA HD        # receptor atom types
ligand_types A P C OA N HD           # ligand atom types

Not relevant to the problem you saw, but there's potentially more issue with the ligand's (SEP) PDBQT file. Not all ligand's atom types are correct (and some polar hydrogens are potentially missing). If the ligand was prepared from an atomistic (all-atom) structure, the amine group will have 2 more hydrogens with atom type HD