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ccsb-scripps / AutoDock-Vina

AutoDock Vina
http://vina.scripps.edu
Apache License 2.0
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Unable to execute. #10

Closed debanjansen48 closed 3 years ago

debanjansen48 commented 3 years ago

issued the following comand

vina12 i renamed and put it in the folder

the config file contains receptor ligand info

"receptor=rec.pdbqt ligand=lig.pdbqt center_x = 27.898 center_y = 5.175 center_z = 59.160 size_x = 25 size_y = 25 size_z = 25 exhaustiveness=50"

./vina12 --config config.txt --maps rec.*.map --scoring vinardo --out lig_out.pdbqt --cpu 8 Command line parse error: too many positional options have been specified on the command line

diogomart commented 3 years ago

Hi,

try changing --maps rec.*.map to --maps rec

debanjansen48 commented 3 years ago

lower_isomer-2/Vina12$ ./vina12 --config config.txt --maps rec --scoring vinardo --out lig_out.pdbqt --cpu 8 #################################################################

If you used AutoDock Vina in your work, please cite:

O. Trott, A. J. Olson,

AutoDock Vina: improving the speed and accuracy of docking

with a new scoring function, efficient optimization and

multithreading, Journal of Computational Chemistry 31 (2010)

455-461

DOI 10.1002/jcc.21334

Please see http://vina.scripps.edu for more information.

#################################################################

ERROR: Cannot specify both receptor and affinity maps at the same time, --flex argument is allowed with receptor or maps.

debanjansen48 commented 3 years ago

Tried with given example files... similar error ......

(base) debanjan@debanjan:~/Downloads/AutoDock-Vina-1.2.0.dev3/example/basic_docking/solution$ ./vina12 --config 1iep_receptor_vina_box.txt --scoring vinardo --maps 1iep_receptor.*.map Command line parse error: too many positional options have been specified on the command line

Correct usage:

Input: --receptor arg rigid part of the receptor (PDBQT) --flex arg flexible side chains, if any (PDBQT) --ligand arg ligand (PDBQT) --batch arg batch ligand (PDBQT) --scoring arg (=vina) scoring function (ad4, vina or vinardo)

Search space (required): --maps arg affinity maps for the autodock4.2 (ad4) or vina scoring function --center_x arg X coordinate of the center (Angstrom) --center_y arg Y coordinate of the center (Angstrom) --center_z arg Z coordinate of the center (Angstrom) --size_x arg size in the X dimension (Angstrom) --size_y arg size in the Y dimension (Angstrom) --size_z arg size in the Z dimension (Angstrom)

Output (optional): --out arg output models (PDBQT), the default is chosen based on the ligand file name --dir arg output directory for batch mode --write_maps arg output filename (directory + prefix name) for maps. Option --force_even_voxels may be needed to comply with .map format

Misc (optional): --cpu arg (=0) the number of CPUs to use (the default is to try to detect the number of CPUs or, failing that, use 1) --seed arg (=0) explicit random seed --exhaustiveness arg (=8) exhaustiveness of the global search (roughly proportional to time): 1+ --max_evals arg (=0) number of evaluations in each MC run (if zero, which is the default, the number of MC steps is based on heuristics) --num_modes arg (=9) maximum number of binding modes to generate --min_rmsd arg (=1) minimum RMSD between output poses --energy_range arg (=3) maximum energy difference between the best binding mode and the worst one displayed (kcal/mol) --spacing arg (=0.375) grid spacing (Angstrom) --verbosity arg (=1) verbosity (0=no output, 1=normal, 2=verbose)

Configuration file (optional): --config arg the above options can be put here

Information (optional): --help display usage summary --help_advanced display usage summary with advanced options --version display program version

(base) debanjan@debanjan:~/Downloads/AutoDock-Vina-1.2.0.dev3/example/basic_docking/solution$ ./vina12 --config 1iep_receptor_vina_box.txt --scoring vinardo --maps 1iep_receptor.*.map Command line parse error: too many positional options have been specified on the command line

Correct usage:

Input: --receptor arg rigid part of the receptor (PDBQT) --flex arg flexible side chains, if any (PDBQT) --ligand arg ligand (PDBQT) --batch arg batch ligand (PDBQT) --scoring arg (=vina) scoring function (ad4, vina or vinardo)

Search space (required): --maps arg affinity maps for the autodock4.2 (ad4) or vina scoring function --center_x arg X coordinate of the center (Angstrom) --center_y arg Y coordinate of the center (Angstrom) --center_z arg Z coordinate of the center (Angstrom) --size_x arg size in the X dimension (Angstrom) --size_y arg size in the Y dimension (Angstrom) --size_z arg size in the Z dimension (Angstrom)

Output (optional): --out arg output models (PDBQT), the default is chosen based on the ligand file name --dir arg output directory for batch mode --write_maps arg output filename (directory + prefix name) for maps. Option --force_even_voxels may be needed to comply with .map format

Misc (optional): --cpu arg (=0) the number of CPUs to use (the default is to try to detect the number of CPUs or, failing that, use 1) --seed arg (=0) explicit random seed --exhaustiveness arg (=8) exhaustiveness of the global search (roughly proportional to time): 1+ --max_evals arg (=0) number of evaluations in each MC run (if zero, which is the default, the number of MC steps is based on heuristics) --num_modes arg (=9) maximum number of binding modes to generate --min_rmsd arg (=1) minimum RMSD between output poses --energy_range arg (=3) maximum energy difference between the best binding mode and the worst one displayed (kcal/mol) --spacing arg (=0.375) grid spacing (Angstrom) --verbosity arg (=1) verbosity (0=no output, 1=normal, 2=verbose)

Configuration file (optional): --config arg the above options can be put here

Information (optional): --help display usage summary --help_advanced display usage summary with advanced options --version display program version

(base) debanjan@debanjan:~/Downloads/AutoDock-Vina-1.2.0.dev3/example/basic_docking/solution$ vina12 --config 1iep_receptor_vina_box.txt --scoring vinardo --maps 1iep_receptor.*.map Command line parse error: too many positional options have been specified on the command line

Correct usage:

Input: --receptor arg rigid part of the receptor (PDBQT) --flex arg flexible side chains, if any (PDBQT) --ligand arg ligand (PDBQT) --batch arg batch ligand (PDBQT) --scoring arg (=vina) scoring function (ad4, vina or vinardo)

Search space (required): --maps arg affinity maps for the autodock4.2 (ad4) or vina scoring function --center_x arg X coordinate of the center (Angstrom) --center_y arg Y coordinate of the center (Angstrom) --center_z arg Z coordinate of the center (Angstrom) --size_x arg size in the X dimension (Angstrom) --size_y arg size in the Y dimension (Angstrom) --size_z arg size in the Z dimension (Angstrom)

Output (optional): --out arg output models (PDBQT), the default is chosen based on the ligand file name --dir arg output directory for batch mode --write_maps arg output filename (directory + prefix name) for maps. Option --force_even_voxels may be needed to comply with .map format

Misc (optional): --cpu arg (=0) the number of CPUs to use (the default is to try to detect the number of CPUs or, failing that, use 1) --seed arg (=0) explicit random seed --exhaustiveness arg (=8) exhaustiveness of the global search (roughly proportional to time): 1+ --max_evals arg (=0) number of evaluations in each MC run (if zero, which is the default, the number of MC steps is based on heuristics) --num_modes arg (=9) maximum number of binding modes to generate --min_rmsd arg (=1) minimum RMSD between output poses --energy_range arg (=3) maximum energy difference between the best binding mode and the worst one displayed (kcal/mol) --spacing arg (=0.375) grid spacing (Angstrom) --verbosity arg (=1) verbosity (0=no output, 1=normal, 2=verbose)

Configuration file (optional): --config arg the above options can be put here

Information (optional): --help display usage summary --help_advanced display usage summary with advanced options --version display program version

(base) debanjan@debanjan:~/Downloads/AutoDock-Vina-1.2.0.dev3/example/basic_docking/solution$ vina12 --config 1iep_receptor_vina_box.txt --maps 1iep_receptor.*.map Command line parse error: too many positional options have been specified on the command line

Correct usage:

Input: --receptor arg rigid part of the receptor (PDBQT) --flex arg flexible side chains, if any (PDBQT) --ligand arg ligand (PDBQT) --batch arg batch ligand (PDBQT) --scoring arg (=vina) scoring function (ad4, vina or vinardo)

Search space (required): --maps arg affinity maps for the autodock4.2 (ad4) or vina scoring function --center_x arg X coordinate of the center (Angstrom) --center_y arg Y coordinate of the center (Angstrom) --center_z arg Z coordinate of the center (Angstrom) --size_x arg size in the X dimension (Angstrom) --size_y arg size in the Y dimension (Angstrom) --size_z arg size in the Z dimension (Angstrom)

Output (optional): --out arg output models (PDBQT), the default is chosen based on the ligand file name --dir arg output directory for batch mode --write_maps arg output filename (directory + prefix name) for maps. Option --force_even_voxels may be needed to comply with .map format

Misc (optional): --cpu arg (=0) the number of CPUs to use (the default is to try to detect the number of CPUs or, failing that, use 1) --seed arg (=0) explicit random seed --exhaustiveness arg (=8) exhaustiveness of the global search (roughly proportional to time): 1+ --max_evals arg (=0) number of evaluations in each MC run (if zero, which is the default, the number of MC steps is based on heuristics) --num_modes arg (=9) maximum number of binding modes to generate --min_rmsd arg (=1) minimum RMSD between output poses --energy_range arg (=3) maximum energy difference between the best binding mode and the worst one displayed (kcal/mol) --spacing arg (=0.375) grid spacing (Angstrom) --verbosity arg (=1) verbosity (0=no output, 1=normal, 2=verbose)

Configuration file (optional): --config arg the above options can be put here

Information (optional): --help display usage summary --help_advanced display usage summary with advanced options --version display program version

(base) debanjan@debanjan:~/Downloads/AutoDock-Vina-1.2.0.dev3/example/basic_docking/solution$ vina12 --config 1iep_receptor_vina_box.txt --scoring vinardo --maps 1iep_receptor #################################################################

If you used AutoDock Vina in your work, please cite:

O. Trott, A. J. Olson,

AutoDock Vina: improving the speed and accuracy of docking

with a new scoring function, efficient optimization and

multithreading, Journal of Computational Chemistry 31 (2010)

455-461

DOI 10.1002/jcc.21334

Please see http://vina.scripps.edu for more information.

#################################################################

Input: --receptor arg rigid part of the receptor (PDBQT) --flex arg flexible side chains, if any (PDBQT) --ligand arg ligand (PDBQT) --batch arg batch ligand (PDBQT) --scoring arg (=vina) scoring function (ad4, vina or vinardo)

Search space (required): --maps arg affinity maps for the autodock4.2 (ad4) or vina scoring function --center_x arg X coordinate of the center (Angstrom) --center_y arg Y coordinate of the center (Angstrom) --center_z arg Z coordinate of the center (Angstrom) --size_x arg size in the X dimension (Angstrom) --size_y arg size in the Y dimension (Angstrom) --size_z arg size in the Z dimension (Angstrom)

Output (optional): --out arg output models (PDBQT), the default is chosen based on the ligand file name --dir arg output directory for batch mode --write_maps arg output filename (directory + prefix name) for maps. Option --force_even_voxels may be needed to comply with .map format

Misc (optional): --cpu arg (=0) the number of CPUs to use (the default is to try to detect the number of CPUs or, failing that, use 1) --seed arg (=0) explicit random seed --exhaustiveness arg (=8) exhaustiveness of the global search (roughly proportional to time): 1+ --max_evals arg (=0) number of evaluations in each MC run (if zero, which is the default, the number of MC steps is based on heuristics) --num_modes arg (=9) maximum number of binding modes to generate --min_rmsd arg (=1) minimum RMSD between output poses --energy_range arg (=3) maximum energy difference between the best binding mode and the worst one displayed (kcal/mol) --spacing arg (=0.375) grid spacing (Angstrom) --verbosity arg (=1) verbosity (0=no output, 1=normal, 2=verbose)

Configuration file (optional): --config arg the above options can be put here

Information (optional): --help display usage summary --help_advanced display usage summary with advanced options --version display program version

ERROR: Missing ligand(s).

atillack commented 3 years ago

@debanjansen48 You almost have it working :-) The 1iep_receptor_vina_box.txt example config file only contains the parameters for the search box but not the ligand which you would need to specify in this example (i.e. --ligand 1iep_ligand.pdbqt).

Here is our writeup for this example: https://autodock-vina.readthedocs.io/en/latest/docking_basic.html#running-autodock-vina

BJWiley233 commented 2 years ago

I am having a prefix map issue. How in the "Hello World" does this not work?

% ls Q00534_fill.*.map                                                           
Q00534_fill.A.map       Q00534_fill.HD.map      Q00534_fill.NA.map      Q00534_fill.d.map
Q00534_fill.C.map       Q00534_fill.N.map       Q00534_fill.OA.map      Q00534_fill.e.map
vina --flex Q00534_fill.BL00010001_ligand_conect.fixed.out_flex.pdbqt --ligand trilaciclib.pdbqt --maps Q00534_fill --scoring vina --exhaustiveness 32 --out Q00534_fill_flex_trilaciclib_vina_out.pdbqt

Scoring function : vina
Flex receptor: Q00534_fill.BL00010001_ligand_conect.fixed.out_flex.pdbqt
Ligand: trilaciclib.pdbqt
Exhaustiveness: 32
CPU: 0
Verbosity: 1

Reading Vina maps ... 
ERROR: No *.map files with prefix "Q00534_fill"
BJWiley233 commented 2 years ago

I added some debug print lines to print out the atom type and file name. This atom types don't match those normally from any sort of run Usage: prepare_receptor4.py -r filename. Is there a new prepare_receptor for vina?

CHECKING atom type: "C_H"

File name: "Q00534_fill.C_H.map"

CHECKING atom type: "C_P"

File name: "Q00534_fill.C_P.map"

CHECKING atom type: "N_P"

File name: "Q00534_fill.N_P.map"

CHECKING atom type: "N_D"

File name: "Q00534_fill.N_D.map"

CHECKING atom type: "N_A"

File name: "Q00534_fill.N_A.map"

CHECKING atom type: "N_DA"

File name: "Q00534_fill.N_DA.map"

CHECKING atom type: "O_P"

File name: "Q00534_fill.O_P.map"

CHECKING atom type: "O_D"

File name: "Q00534_fill.O_D.map"

CHECKING atom type: "O_A"

File name: "Q00534_fill.O_A.map"

CHECKING atom type: "O_DA"

File name: "Q00534_fill.O_DA.map"

CHECKING atom type: "S_P"

File name: "Q00534_fill.S_P.map"

CHECKING atom type: "P_P"

File name: "Q00534_fill.P_P.map"

CHECKING atom type: "F_H"

File name: "Q00534_fill.F_H.map"

CHECKING atom type: "Cl_H"

File name: "Q00534_fill.Cl_H.map"

CHECKING atom type: "Br_H"

File name: "Q00534_fill.Br_H.map"

CHECKING atom type: "I_H"

File name: "Q00534_fill.I_H.map"

CHECKING atom type: "Si"

File name: "Q00534_fill.Si.map"

CHECKING atom type: "At"

File name: "Q00534_fill.At.map"

CHECKING atom type: "Met_D"

File name: "Q00534_fill.Met_D.map"

CHECKING atom type: "C_H"

File name: "Q00534_fill.C_H.map"

CHECKING atom type: "C_P"

File name: "Q00534_fill.C_P.map"

CHECKING atom type: "W"

File name: "Q00534_fill.W.map"
BJWiley233 commented 2 years ago

OK this only works for ad4 scoring function. This needs to be added to readthedocs as a warning under https://autodock-vina.readthedocs.io/en/latest/docking_basic.html?highlight=map#a-using-autodock4-forcefield :smile: