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ccsb-scripps / AutoDock-Vina

AutoDock Vina
http://vina.scripps.edu
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Flexible docking of Autodock using vina #292

Open Kapalisuri opened 3 months ago

Kapalisuri commented 3 months ago

I want to run flexible docking using vina but ad4 as a scoring function. I have prepared by receptor using prepare_receptor.py and ligand using prepare_ligand4.py. The command I am using to run it is : ./vina_1.2.5_linux_x86_64 \ --receptor 7MYI_receptor_rigid.pdbqt \ --flex 7MYI_receptor_flex.pdbqt \ --ligand 7MYI_cleaned_lig.pdbqt \ --scoring ad4 \ --out 7MYI_ligand_flex_ad4_out.pdbqt --exhaustiveness 32 \ --config 7MYI_receptor_rigid_vina_box.txt and the error I am getting is : Output will be 7MYI_cleaned_lig_out.pdbqt Scoring function : vina Rigid receptor: 7MYI_receptor_rigid.pdbqt Flex receptor: 7MYI_receptor_flex.pdbqt Ligand: 7MYI_cleaned_lig.pdbqt Grid center: X 4.94066e-324 Y 1.03978e-312 Z 0 Grid size : X 0 Y 0 Z 2.52517e-312 Grid space : 0.375 Exhaustiveness: 8 CPU: 0 Verbosity: 1

An error occurred:

Vina runtime error: Grid box dimensions must be greater than 0 Angstrom .

Please report bugs through the Issue Tracker on GitHub (https://github.com/ccsb-scripps/AutoDock-Vina/issues)., so that this problem can be resolved. The reproducibility of the error may be vital, so please remember to include the following in your problem report:

Thank you! ./adock1.sh: line 12: --scoring: command not found ./adock1.sh: line 14: --exhaustiveness: command not found, Kindly help me fix the error. How I can perform flexible docking for Autodock using vina. The tutorial I followed is: https://autodock-vina.readthedocs.io/en/latest/docking_flexible.html 7MYI_receptor_rigid_vina_box.txt

rwxayheee commented 3 months ago

Hi @Kapalisuri if you want the scoring function to be ad4, you need to provide the prefix of the pre-computed affinity maps via --maps instead of --receptor. You can find specific instructions from sections 3 and 4.a in the tutorial you use One more thing: if your command spans multiple lines, you might want to put a backslash \ at the end of lines if they are not the end of the command

Kapalisuri commented 3 months ago

./vina_1.2.5_linux_x86_64 \

--flex 7MYI_receptor_flex.pdbqt \

--ligand 7MYI_cleaned_lig.pdbqt \

--maps 7MYI_receptor_rigid \

--scoring ad4 \

--exhaustiveness 32 \

--out 7MYI_ligand_flex_ad4_out.pdbqt

I have corrected the command but still I am getting the error as: ERROR: Affinity map for atom type OA is not present. Further the script was used to prepare the receptor was: /home/arul/Kapali/MDDP/mgltools_x86_64Linux2_1.5.7/bin/pythonsh prepare_flexreceptor.py -r 7MYI.pdbqt -s ASP228_ASP32_TYR71_PHE108_SER35 -g 7MYI_receptor_rigid.pdbqt -x 7MYI_receptor_flex.pdbqt /home/arul/Kapali/MDDP/mgltools_x86_64Linux2_1.5.7/bin/pythonsh /home/arul/Kapali/MDDP/mgltools_x86_64Linux2_1.5.7/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_gpf4.py -l 7MYI_cleaned_lig.pdbqt -r 7MYI_receptor_rigid.pdbqt -y /home/arul/Kapali/MDDP/BACE1_HUMAN/docking_output_B/2QMF/flex/x86_64Linux2/autogrid4 -p 7MYI_receptor_rigid.gpf -l 7MYI_receptor_rigid.glg.

If I am using the script: prepare_flexreceptor4.py; this error is appearing

setting PYTHONHOME environment

WARNING: no residue named ASP228

WARNING: no residue named ASP32

WARNING: no residue named TYR71

WARNING: no residue named PHE108

WARNING: no residue named SER35

setting PYTHONHOME environment

Kindly help me resolve.

On Fri, Mar 22, 2024 at 1:49 PM Amy He @.***> wrote:

Hi @Kapalisuri https://github.com/Kapalisuri if you want the scoring function to be ad4, you need to provide the prefix of the pre-computed affinity maps via --maps instead of --receptor. One more thing: if your command spans multiple lines, you might want to put a backslash \ at the end of lines if they are not the end of the command

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rwxayheee commented 3 months ago

Hi @Kapalisuri

Does it work if you specify the flex receptor file for prepare_gpf4.py? Something like

/home/arul/Kapali/MDDP/mgltools_x86_64Linux2_1.5.7/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_gpf4.py
-l 7MYI_cleaned_lig.pdbqt -x 7MYI_receptor_flex.pdbqt -r 7MYI_receptor_rigid.pdbqt

The option -x 7MYI_receptor_flex.pdbqt adds atom types from the flex receptor file to ligand_types in the GPF file, which is like the todo list of atom types to compute affinity maps for. This might fix the missing OA map problem. Alternatively, you can manually edit the GPF file according to your needs

Kapalisuri commented 3 months ago

Thanks it worked!

On Fri, Mar 22, 2024 at 10:04 PM Amy He @.***> wrote:

Hi @Kapalisuri https://github.com/Kapalisuri

Does it work if you specify the flex receptor file for prepare_gpf4.py? Something like

/home/arul/Kapali/MDDP/mgltools_x86_64Linux2_1.5.7/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_gpf4.py -l 7MYI_cleaned_lig.pdbqt -x 7MYI_receptor_flex.pdbqt -r 7MYI_receptor_rigid.pdbqt

The option -x 7MYI_receptor_flex.pdbqt adds atom types from the flex receptor file to ligand_types in the GPF file, which is like the todo list of atom types to compute affinity maps for. This might fix the missing OA map problem. Alternatively, you can manually edit the GPF file according to your needs

— Reply to this email directly, view it on GitHub https://github.com/ccsb-scripps/AutoDock-Vina/issues/292#issuecomment-2015470809, or unsubscribe https://github.com/notifications/unsubscribe-auth/BG5MWNY7TL6O4D4QWH5I7LLYZRMSZAVCNFSM6AAAAABFC2XLH6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMJVGQ3TAOBQHE . You are receiving this because you were mentioned.Message ID: @.***>

Kapalisuri commented 2 months ago

Hi, I have a query, I have been using vina both for flexible docking of vina and autodock, after docking my ligand is getting broken. The original image of the ligand is Screenshot 2024-04-26 at 3.35.43.png and the other one is after docking. I am also attaching the image containing the 10 binding poses but that is also broken (Screenshot 2024-04-26 at 3.39.50.png) Can you tell me the possible reason behind it? How should I proceed further?

Kindly solve my query, I will be thankful.

Regards Kapali

On Sat, Mar 23, 2024 at 12:35 PM Kapali Suri @.***> wrote:

Thanks it worked!

On Fri, Mar 22, 2024 at 10:04 PM Amy He @.***> wrote:

Hi @Kapalisuri https://github.com/Kapalisuri

Does it work if you specify the flex receptor file for prepare_gpf4.py? Something like

/home/arul/Kapali/MDDP/mgltools_x86_64Linux2_1.5.7/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_gpf4.py -l 7MYI_cleaned_lig.pdbqt -x 7MYI_receptor_flex.pdbqt -r 7MYI_receptor_rigid.pdbqt

The option -x 7MYI_receptor_flex.pdbqt adds atom types from the flex receptor file to ligand_types in the GPF file, which is like the todo list of atom types to compute affinity maps for. This might fix the missing OA map problem. Alternatively, you can manually edit the GPF file according to your needs

— Reply to this email directly, view it on GitHub https://github.com/ccsb-scripps/AutoDock-Vina/issues/292#issuecomment-2015470809, or unsubscribe https://github.com/notifications/unsubscribe-auth/BG5MWNY7TL6O4D4QWH5I7LLYZRMSZAVCNFSM6AAAAABFC2XLH6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMJVGQ3TAOBQHE . You are receiving this because you were mentioned.Message ID: @.***>

rwxayheee commented 2 months ago

Hi @Kapalisuri We can't receive pictures from email. Is your output similar to This issue? If not please kindly share the inputs/outputs and we can have a look :>

Kapalisuri commented 2 months ago

Yes, the output is similar to this issue.

Regards Kapali

On Fri, Apr 26, 2024 at 9:39 PM Amy He @.***> wrote:

Hi @Kapalisuri https://github.com/Kapalisuri We can't receive pictures from email. Is your output similar to This issue https://github.com/ccsb-scripps/AutoDock-Vina/issues/304#issue-2265605855? If not please kindly share the inputs/outputs and we can have a look :>

— Reply to this email directly, view it on GitHub https://github.com/ccsb-scripps/AutoDock-Vina/issues/292#issuecomment-2079685874, or unsubscribe https://github.com/notifications/unsubscribe-auth/BG5MWN4PIMNVQPQQUMPBDMTY7J343AVCNFSM6AAAAABFC2XLH6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANZZGY4DKOBXGQ . You are receiving this because you were mentioned.Message ID: @.***>