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

 

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