[Chimera-users] ViewDock: flexible receptor residues in different chains

Jérôme Hénin jerome.henin at ibpc.fr
Wed Mar 6 08:27:03 PST 2013

Hi everyone,

When viewing Autodock Vina results in ViewDock, I hit a problem that I think is due to insufficient parsing of the PDBQT file. I have flexible receptor residues in two identical chains, say, Leu15 in chain A and Leu15 in chain B - these sidechains are part of the PDBQT file. However, ViewDock apparently ignores chain identifiers in that file, so it is unable to distinguish between these two residues, and it creates mangled bonds linking them while some other bonds are missing.

I don't know how much work it would be to parse chain identifiers from the PDBQT file, I would have a go at it if I was more of a Python person, but I really am not.


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