Dear UCSF Hello, I'm Choi Hwan. I'm a college student majoring in molecular design research in Korea. I'm inquiring about a problem in the process of making a pdbqt file during the research project. First of all, the contents are as follows. I made a total of two ligand.pdbqt. (1) Called Lingand(4YZN) to chimera as sdf file and ran autodock vina. That way, I can see that 4YZN.pdb and 4YZN.pdbqt are created. (2) We also used Autodock tools to make 4YZN.pdbqt of 4YZN.pdb generated in the process above. Autodock tools used here directly used prepare_ligand4.py in the path where chimera was installed. As a result, the format of the three pdbqt made was different. The 4YZN.pdbqt made in chimera had 6 active torsions and the 4YZN.pdbqt made using Autodock tools had 7 active torsions. The result was that the vina docking results were different. As a result of docking, the (1) pdbqt made in chimera was better suited for vina docking. I want to create the pdbqt format generated by chimera. Since we need to make a large amount of compound into pdbqt, could you tell me how to get pdbqt without using chimera GUI? I am using linux. Or I would like to know if I missed anything in the process of making sdf -> pdb -> pdbqt in chimera. (using chimera 1.17.3)
Hello, In Chimera's Autodock Vina tool, to create pdbqt files, Chimera runs ligand and receptor preparation scripts that were originally obtained from the Autodock Vina website several years ago. At that website, there were these two python scripts as well as instructions on how to run them directly from the system command line (with no involvement of Chimera). However, I can no longer find these webpages on the Autodock Vina website. However, just today from google search I found a 2021 publication that links to copies of the prep scripts and that also has some brief description of how to run them directly. Please see this article and links therein to download the ligand-prep and receptor-prep python scripts: <https://bioinformaticsreview.com/20200716/prepare-receptor-and-ligand-files-for-docking-using-python-scripts/> As far as I know these would be the same scripts that are somewhere in the Chimera installation, but the above is how to access them independent of Chimera. The comments in the scripts also describe more of the command-line flags if you want to use different options than in that brief article. As for the copies of the scripts in Chimera, I don't know where in the Chimera installation they are kept (maybe somebody else can comment on this in case they aren't exactly the same as the ones in that article). I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 19, 2025, at 11:45 PM, Healer Choi via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear UCSF
Hello, I'm Choi Hwan. I'm a college student majoring in molecular design research in Korea.
I'm inquiring about a problem in the process of making a pdbqt file during the research project.
First of all, the contents are as follows. I made a total of two ligand.pdbqt. (1) Called Lingand(4YZN) to chimera as sdf file and ran autodock vina. That way, I can see that 4YZN.pdb and 4YZN.pdbqt are created. (2) We also used Autodock tools to make 4YZN.pdbqt of 4YZN.pdb generated in the process above. Autodock tools used here directly used prepare_ligand4.py in the path where chimera was installed.
As a result, the format of the three pdbqt made was different. The 4YZN.pdbqt made in chimera had 6 active torsions and the 4YZN.pdbqt made using Autodock tools had 7 active torsions. The result was that the vina docking results were different. As a result of docking, the (1) pdbqt made in chimera was better suited for vina docking.
I want to create the pdbqt format generated by chimera. Since we need to make a large amount of compound into pdbqt, could you tell me how to get pdbqt without using chimera GUI? I am using linux.
Or I would like to know if I missed anything in the process of making sdf -> pdb -> pdbqt in chimera. (using chimera 1.17.3) <4YZN_Chimera.pdbqt><4YZN_Autodocktools.pdbqt>
It looks like you could also get them from https://github.com/jaimergp/autodocktools-prepare-py3k/tree/master/AutoDockT... and those versions might work with Python 3. --Eric Eric Pettersen UCSF Computer Graphics Lab
On Feb 20, 2025, at 12:40 PM, Elaine Meng via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hello, In Chimera's Autodock Vina tool, to create pdbqt files, Chimera runs ligand and receptor preparation scripts that were originally obtained from the Autodock Vina website several years ago. At that website, there were these two python scripts as well as instructions on how to run them directly from the system command line (with no involvement of Chimera). However, I can no longer find these webpages on the Autodock Vina website.
However, just today from google search I found a 2021 publication that links to copies of the prep scripts and that also has some brief description of how to run them directly. Please see this article and links therein to download the ligand-prep and receptor-prep python scripts:
As far as I know these would be the same scripts that are somewhere in the Chimera installation, but the above is how to access them independent of Chimera. The comments in the scripts also describe more of the command-line flags if you want to use different options than in that brief article.
As for the copies of the scripts in Chimera, I don't know where in the Chimera installation they are kept (maybe somebody else can comment on this in case they aren't exactly the same as the ones in that article).
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 19, 2025, at 11:45 PM, Healer Choi via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear UCSF
Hello, I'm Choi Hwan. I'm a college student majoring in molecular design research in Korea.
I'm inquiring about a problem in the process of making a pdbqt file during the research project.
First of all, the contents are as follows. I made a total of two ligand.pdbqt. (1) Called Lingand(4YZN) to chimera as sdf file and ran autodock vina. That way, I can see that 4YZN.pdb and 4YZN.pdbqt are created. (2) We also used Autodock tools to make 4YZN.pdbqt of 4YZN.pdb generated in the process above. Autodock tools used here directly used prepare_ligand4.py in the path where chimera was installed.
As a result, the format of the three pdbqt made was different. The 4YZN.pdbqt made in chimera had 6 active torsions and the 4YZN.pdbqt made using Autodock tools had 7 active torsions. The result was that the vina docking results were different. As a result of docking, the (1) pdbqt made in chimera was better suited for vina docking.
I want to create the pdbqt format generated by chimera. Since we need to make a large amount of compound into pdbqt, could you tell me how to get pdbqt without using chimera GUI? I am using linux.
Or I would like to know if I missed anything in the process of making sdf -> pdb -> pdbqt in chimera. (using chimera 1.17.3) <4YZN_Chimera.pdbqt><4YZN_Autodocktools.pdbqt>
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participants (3)
-
Elaine Meng -
Eric Pettersen -
Healer Choi