[Dock-fans] ligand preparation

Nadeem A Vellore nvellor at g.clemson.edu
Tue Nov 29 11:56:17 PST 2011

Dear Dock users,

I am new to DOCK program. I went thru the tutorials and found the way to
prepare ligand using
1. Chimera tools
2. ZINC server

Is there a way to prepare the ligands (if more than 1000s) in a stand-alone
program, basically to calculate the charges and write a mol2 file. I have a
ligprep format ligands that i would like to convert to mol2 format with
proper charges.

I assume antechamber tools included in chimera can do this on a command
prompt mode. Any ideas.

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