Docking with auto dock fails for a ligand containing a Boron atom
Dear All, I’m trying to dock a ligand containing a boronate substituent using Auto Dock Vina within Chimera v. 1.13.1 The process fails as the B in the pdb instance is not recognized for Boron and the following syntax error is printed “Parse error on line 27 in file "ligand.pdbqt": ATOM syntax incorrect: "B" is not a valid AutoDock type. Note that AutoDock atom types are case-sensitive” Is there any way to overcome this? Are there newer/different libraries that inlcude also Boron element I can update my ADV with? Many thanks for your time and best regards, marco -- Marco Patrone – PhD Biocrystallography Unit Division of Immunology, Transplantation, and Infectious Disease (DITID) DIBIT – San Raffaele Scientific Institute Via Olgettina, 58 20132 Milano Italy phone: +39 0226434921 fax: +39 0226434153 http://www.hsr.it/research/organzation/massimo-degano [https://p.hsr.it/5xmille/b2024.jpg]<https://www.5xmille.org/?utm_source=firmamail&utm_medium=email&utm_campaign=5xmille2024> CODICE FISCALE 07636600962 Scopri di più su www.5xmille.org<https://www.5xmille.org/?utm_source=firmamail&utm_medium=email&utm_campaign=5xmille2024> Rispetta l’ambiente: non stampare questa mail se non è necessario. Respect the environment: print this email only if necessary.
Dear Marco, Sorry no, there is no way as far as I know. Also note that using Chimera''s Autodock Vina tool is not recommended for most research purposes, see the lower part of the gray box warning on the help page. <https://www.rbvi.ucsf.edu/chimera/current/docs/ContributedSoftware/vina/vina.html> Depending on your project, it may be better to run Autodock Vina directly (not through Chimera) to avoid these limitations. We are not the Autodock Vina developers, so you could try looking at their website and documentation to see if there is any way you can include boron. My guess is probably not, though. You might have to change it to carbon or whatever you think is most similar to estimate the interactions. <https://vina.scripps.edu/> Regards, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 15, 2024, at 6:36 AM, Patrone Marco via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear All, I’m trying to dock a ligand containing a boronate substituent using Auto Dock Vina within Chimera v. 1.13.1
The process fails as the B in the pdb instance is not recognized for Boron and the following syntax error is printed
“Parse error on line 27 in file "ligand.pdbqt": ATOM syntax incorrect: "B" is not a valid AutoDock type. Note that AutoDock atom types are case-sensitive”
Is there any way to overcome this? Are there newer/different libraries that inlcude also Boron element I can update my ADV with?
Many thanks for your time and best regards, marco
participants (2)
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Elaine Meng -
Patrone Marco