I ran into this problem while running the program, and I personally couldn't solve it Traceback (most recent call last): File "/usr/bin/metaldock", line 6, in main() File "/home/Gary/anaconda3/envs/MetalDock/lib/python3.11/site-packages/src/metal_dock/main.py", line 18, in main docking(par) File "/home/Gary/anaconda3/envs/MetalDock/lib/python3.11/site-packages/src/metal_dock/docking.py", line 50, in docking shutil.copyfile(input_pdb, output_pdb) File "/home/Gary/anaconda3/envs/MetalDock/lib/python3.11/shutil.py", line 236, in copyfile raise SameFileError("{!r} and {!r} are the same file".format(src, dst)) shutil.SameFileError: '/home/Gary/Desktop/3iai-pro-Zn.pdb' and '/home/Gary/Desktop/3iai-pro-Zn.pdb' are the same file

Could you share with me your input files and output files? I can then better deduce what the problem is.

Thank you for your reply, and I am extremely grateful for your help. I am learning docking using different software, but other software cannot effectively dock metal complexes. This is my file. Then I ran metal - i ini I haven't changed the path in the ini file. Optimized using AMF. Linux system. Python 3.11.7

At 2024-03-27 18:38:22, "MatthijsHak" @.***> wrote:

Could you share with me your input files and output files? I can then better deduce what the problem is.

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***> [DEFAULT] metal_symbol = Pt method = dock ncpu = 12

[PROTEIN] pdb_file = /home/Gary/Desktop/3iai-pro-Zn.pdb pH = 6.2 clean_pdb = True

[QM] engine = ADF basis_set = QZ4P functional_type = MetaHYBRID functional = TPSSH dispersion = GRIMME3 BJDAMP solvent = water

[METAL_COMPLEX] geom_opt = True xyz_file = /home/Gary/Desktop/1/Pt11.xyz charge = 2 spin = 0 vacant_site = True

[DOCKING] ga_dock = True box_size = 27 random_pos = True num_poses = 20

Thanks for your reply. But could you send me zip file of the whole directory? I can then better understand where the problem is coming from.

Dear，

I have written the code into file.txt. Are you referring to these two files in file.zip? I also compressed the metal files in the Python environment

At 2024-03-27 19:11:02, "MatthijsHak" @.***> wrote:

Thanks for your reply. But could you send me zip file of the whole directory? I can then better understand where the problem is coming from.

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>

从网易163邮箱发来的超大附件推荐客户端极速下载 file.zip (294B, 2024年4月11日 19:34 到期) 下载 file.txt (999B, 2024年4月11日 19:34 到期) 下载 MetalDock.zip (283.13M, 2024年4月11日 19:40 到期) 下载

Unfortunatley, I can't access the files for some reason. Try to upload them from the comment section on the Github site. That will most likely solve this issue.

Try compressing the file in this format 666.zip

Dear Sir，

I uploaded it to GitHub

At 2024-03-27 19:47:49, "MatthijsHak" @.***> wrote:

Unfortunatley, I can't access the files for some reason. Try to upload them from the comment section on the Github site. That will most likely solve this issue.

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>

Hi,

The error came from the fact that the path was not correctly set in the code due to the files being in the input dir. I adjusted this such that it now runs smoothly when you have the pdb and xyz files in the same directory as the .ini file, or if you specify the full path. By downloading the latest repo your calculation should work.

Hi， Thank you for solving my previous problem. I have now encountered a new one. My program ran for four days and encountered the following error message

[01.04|20:54:06] JOB plamsjob STARTED [01.04|20:54:06] JOB plamsjob RUNNING

[05.04|17:38:04] JOB plamsjob FINISHED [05.04|17:38:04] Job plamsjob reported warnings. Please check the the output [05.04|17:38:04] JOB plamsjob SUCCESSFUL [05.04|17:38:04] PLAMS run finished. Goodbye

GEOMETRY CONVERGED

Traceback (most recent call last):

File "/usr/bin/metaldock", line 6, in

main()

File "/home/Gary/anaconda3/envs/MetalDock/lib/python3.11/site-packages/src/metal_dock/main.py", line 18, in main

docking(par)

File "/home/Gary/anaconda3/envs/MetalDock/lib/python3.11/site-packages/src/metal_dock/docking.py", line 94, in docking

shutil.copyfile(clean_pdb_in, clean_pdb_out)

File "/home/Gary/anaconda3/envs/MetalDock/lib/python3.11/shutil.py", line 256, in copyfile

with open(src, 'rb') as fsrc:

     ^^^^^^^^^^^^^^^

FileNotFoundError: [Errno 2] No such file or directory: '/media/Gary/5/output/file_prep/clean_3iai-pro-Zn.pdb'

But I found it below this path：/media/Gary/5/output/file_prep/clean_3iai-pro-Zn I don't know where the problem occurred. This file is not in PDB format

Message ID: @.***>

Hi,

I overlooked something, but I adjusted that now as well. With the new repo the docking process now runs smoothly. You should only consider to specify coordinates to center the box where you want it. It does it standard at 0,0,0, which in your case is too far away from the protein.

Let me know if there are still problems.

Hi，

Should coordinate centers be added to the. ini file?

Is this inside?

Ga_dock=True

Box_size=20

Random_pos=True

Num positions=10

I rewrote it based on this' input_examples'. If necessary, should I fill in all the data as required by the input file on your website?

Can the data of protein docking sites measured by Pymol software be directly used?

At 2024-04-09 16:25:10, "MatthijsHak" @.***> wrote:

Hi,

I overlooked something, but I adjusted that now as well. With the new repo the docking process now runs smoothly. You should only consider to specify coordinates to center the box where you want it. It does it standard at 0,0,0, which in your case is too far away from the protein.

Let me know if there are still problems.

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>

The centre of the box for the docking coordinates can be specifed as follow:

[DOCKING] ga_dock = True dock_x = dock_y = dock_z = box_size = 27 random_pos = True num_poses = 5

I am not familiar with this docking sites calculation of Pymol, so I did not implement this. However, it should specify some coordinates. You can always take the centre of an atom to which you think the metal atom is likely to coordinate to, but then just increase the box size a little bit to accommodate for the fact that a part of the box is overlapping with the protein.

Hi，

Can you help me see where the problem is? Is it my little molecule, right?

This is an error. I have attached the error file

[09.04|18:39:08] PLAMS working folder: /media/Gary/5/output/QM/geom_opt/plams_workdir

[09.04|18:39:08] JOB plamsjob STARTED

[09.04|18:39:08] JOB plamsjob RUNNING

[10.04|09:14:34] WARNING: Job plamsjob finished with nonzero return code

[10.04|09:14:34] JOB plamsjob CRASHED

[10.04|09:14:34] PLAMS run finished. Goodbye

GEOMETRY NOT CONVERGED

PLEASE CHECK THE ams.log FILE IN THE QM DIRECTORY

Message ID: @.***>

Hi，

I also tried using orca, but it didn't converge. Can you recommend a base group for me? I think there may be fewer suitable base groups for platinum testing. (I am a platinum complex) Or can we directly dock without optimizing the molecules.Message ID: @.***>

Hi,

I do not see the whole file as you only printed a part of the ams.log file. A few things to consider with QM optimizations. You already chose a very large basis set and an expensive functional to use. It is often easier to start an initial optimization at a lower level of theory to quickly converge to a structure that is close to a minimum at the higher level of theory. You will then need less iterations at the higher level of theory to eventually converge. I normally start with a GFNxTB pre-optimization (not implemented in MetalDock) before I do any DFT calculations. However, with DFT the structure you provided converged within 63 GOsteps with the following settings:

[QM] engine = ADF basis_set = DZP functional_type = GGA functional = PBE dispersion = GRIMME3 BJDAMP solvent = water

You could increase the basis set to TZP and higher, but remember that that always comes at a cost. Also, our DFT calculations are used to determine the charges for the docking procedure, so I am not 100% sure if you require the highest level of theory for your study case. You can perform some tests, extracting the charges at different level of theories and seeing what the effect is (I would assume not so large). Hopefully this gives you some guidance for your problem.