Docking issue

[Johnson7L]

Dear developer,

I attempted to execute the example from the "MetalDock" paper, which involves the interaction between (A)-19 and 3CLpro. However, I encountered errors during the docking process shown as followed.

GPF> nbp_r_eps 0.25 23.2135 12 6 NA TZ

Overriding non-bonded interaction energies for docking calculation; GPF> nbp_r_eps 2.10 3.8453 12 6 OA Zn

Overriding non-bonded interaction energies for docking calculation; GPF> nbp_r_eps 2.25 7.5914 12 6 SA Zn

Overriding non-bonded interaction energies for docking calculation; GPF> nbp_r_eps 1.00 0.0000 12 6 HD Zn

Overriding non-bonded interaction energies for docking calculation; GPF> nbp_r_eps 2.00 0.0060 12 6 NA Zn

Overriding non-bonded interaction energies for docking calculation; GPF> nbp_r_eps 2.00 0.2966 12 6 N Zn

Overriding non-bonded interaction energies for docking calculation; GPF> nbp_r_eps 2.20 6.7380 12 10 NA Re

Overriding non-bonded interaction energies for docking calculation; GPF> nbp_r_eps 2.25 0.6450 12 10 OA Re

Overriding non-bonded interaction energies for docking calculation; GPF> nbp_r_eps 2.30 3.3090 12 10 SA Re

Overriding non-bonded interaction energies for

Overriding non-bonded interaction energies for docking calculation; Segmentation fault (core dumped) /Documents/MetalDock/src/external/AutoDock/autodock4: creating docking log file ligand_clean_6y2f.dlg /Documents/MetalDock/src/external/AutoDock/autodock4: ERROR: Unknown ligand atom type "2.00.2966"; add parameters for it to the parameter library first! /Documents/MetalDock/src/external/AutoDock/autodock4: Edit the parameter library file "metal_dock.dat" and try again. /Documents/MetalDock/src/external/AutoDock/autodock4: FATAL ERROR: /Documents/MetalDock/src/external/AutoDock/autodock4: Edit the parameter library file "metal_dock.dat" and try again.

/Documents/MetalDock/src/external/AutoDock/autodock4: Unsuccessful Completion.

I sincerely appreciate your assistance in advance.

Regards, Z. LIN

[MatthijsHak]

Dear Lin,

Could you please provide me with all the files, input from you and output generated by MetalDock. From this output alone I can not deduce what went wrong. Thank you in advance.

Regards,

Matthijs

[Johnson7L]

Dear Matthijs,

I sincerely appreciate your response.

The files will be attached to this comment.

Regards, Z. LIN[](url) test.zip

[MatthijsHak]

Dear Z. Lin,

You used an older setting the standard = True. Could you please help me where I used this setting as an example, so that I can delete it. Currently, your settings are running on my computer with the .ini file attached to this comment.

Be aware, you are using the RMSD parameter, but as you do not have a X-ray structure as reference for the Rhenium complex, it uses the geometry optimised coordinates of the metal complex to determine the RMSD, which is in a different local frame than the PDB file.

orca_input_ini.txt

If you encounter any future problems, please do not hesitate to write an issue.

Regards,

Matthijs

[Johnson7L]

Dear Matthijs,

You didn't include the example that involves the "standard = True" parameter. However, I noticed that in the docking.py file located at MetalDock/src/metal_dock/, which was downloaded using the command "git clone https://github.com/MatthijsHak/MetalDock" as per the installation instructions provided on the official documentation at "https://metaldock.readthedocs.io/en/latest/installation/", there is a line of code that reads "if par.standard == True." In response to this, I took the initiative to add "the standard = True" parameter on my own.

I am sincerely grateful for your unwavering assistance and patience.

Regards, Zexiong

[MatthijsHak]

Ah okay great to know. I changed that so it should run smoothly now. Let me know if the issue is fixed, then we can close it.

[MatthijsHak]

Sorry I forgot to say, but you should git clone once again, as the source code has been changed.

[Johnson7L]

Dear Matthijs,

After using the new source code, the docking issue still remains.

GPF> nbp_r_eps 0.25 23.2135 12 6 NA TZ

Overriding non-bonded interaction energies for docking calculation; GPF> nbp_r_eps 2.10 3.8453 12 6 OA Zn

Overriding non-bonded interaction energies for docking calculation; GPF> nbp_r_eps 2.25 7.5914 12 6 SA Zn

Overriding non-bonded interaction energies for docking calculation; GPF> nbp_r_eps 1.00 0.0000 12 6 HD Zn

Overriding non-bonded interaction energies for docking calculation; GPF> nbp_r_eps 2.00 0.0060 12 6 NA Zn

Overriding non-bonded interaction energies for docking calculation; GPF> nbp_r_eps 2.00 0.2966 12 6 N Zn

Overriding non-bonded interaction energies for docking calculation; GPF> nbp_r_eps 2.20 6.7380 12 10 NA Re

Overriding non-bonded interaction energies for docking calculation; GPF> nbp_r_eps 2.25 0.6450 12 10 OA Re

Overriding non-bonded interaction energies for docking calculation; GPF> nbp_r_eps 2.30 3.3090 12 10 SA Re

Overriding non-bonded interaction energies for docking calculation; GPF> nbp_r_eps 1.00 4.5020 12 6 HD Re

Overriding non-bonded interaction energies for docking calculation; Segmentation fault (core dumped) /Documents/MetalDock/src/external/AutoDock/autodock4: creating docking log file ligand_clean_6y2f.dlg /Documents/MetalDock/src/external/AutoDock/autodock4: ERROR: Unknown ligand atom type "2.00.2966"; add parameters for it to the parameter library first! /Documents/MetalDock/src/external/AutoDock/autodock4: Edit the parameter library file "metal_dock.dat" and try again. /Documents/MetalDock/src/external/AutoDock/autodock4: FATAL ERROR: /Documents/MetalDock/src/external/AutoDock/autodock4: Edit the parameter library file "metal_dock.dat" and try again.

/Documents/MetalDock/src/external/AutoDock/autodock4: Unsuccessful Completion.

Additionally, there are two typos in the source code. In line 541 of /MetalDock/src/metal_dock/preparedock.py, the "clean{par.nameprotein}.pdb" needs to be edited as " clean{name_protein}.pdb". In line 120 of /MetalDock/src/metal_dock/docking.py", the "d.docking_func(par, par.parameter_set, par.name_ligand, par.name_protein, dock, box_size, energy)" needs to be edited as "d.docking_func(par, dock, box_size, energy)".

Regards, Z.LIN

[MatthijsHak]

Thank you for bringing that to my mention, I immediately changed it. I think the problem was caused by the preparation of the gpf file. I added now to the MetalDock some extra external tools, that may have caused a path problem. For me this now works, hopefully for you as well. Let me know, as I am eager to make it work.

Thank your for helping me making the code better.

Regards,

Matthijs

[Johnson7L]

Dear Matthijs,

I ran again after downloading the new source code and the issue still remained (without path problems).

I attached the all files via this comment, which might be helpful to analyse the cause.

test.zip

Regards, Z.LIN

[MatthijsHak]

For me the code works, but I am able to reproduce your error by commenting out line 546 in prepare_dock.py. As I do not have your complete output, I can not exactly know why this particular line of code is not properly executed.

Could you verify that the MetalDock/src/external/AutoDockTools dir is present. Could you also verify that the ROOT_DIR in environment_variables.py is set correctly. You can do this by adding print(ROOT_DIR) on line 6 in environment_variables.py. You should see the path to MetalDock/src Could you verify that you have python2.7 in your conda environment.

Regards,

Matthijs

[Johnson7L]

Dear Matthijs,

Yeah. You are right. I create a new environment for python2.7 and set a path to it. The docking can run smoothly now.

I am sincerely grateful for your unwavering assiantance and patience!

Regards, Z.LIN

[MatthijsHak]

Dear Zexiong,

Great that it works. I now removed the dependency on python2, so that in the future this error hopefully will not occur anymore. I will close this issue now.

Regards,

Matthijs