[Chimera-users] Failure Running ANTECHAMER

Eric Choi e.choi0309 at gmail.com
Thu Dec 3 22:23:21 PST 2020

To whom it may concern,

My name is Eric Choi and I am currently a student at Ithaca College doing
research about virtual ligand screening where I utilize programs like
Chimera and Dock6.

In my workflow, I use Chimera to prepare ligands (downloaded from the ZINC
database) by adding hydrogens (using the "steric only" method and
"unspecified") and adding charges (AM1-BCC). Then, I run the Dock6 program,
which predicts potential binding geometries and interactions of a molecule
to a target protein. When I add hydrogens and charges to individual ligands
(downloaded from the ZINC database), it works fine. However, when I
downloaded different subsets of molecules (containing 100 ligands to 2000
ligands), an error message popped up saying that ANTECHAMBER failed to run
(please see screenshots below). What does this mean? Is there any way that
I can fix this issue? If a certain ligand is causing this problem, is there
a way to see which one it is?

Thank you very much for your time and help.

Eric Choi
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