Hi Snoze, One of the main uses of the ZINC database is to generate ligand sets for DOCK; I believe you can download mol2 format directly from ZINC, and that the molecules already have hydrogens and charges. See http://zinc.docking.org/ But maybe you wanted to use Antechamber inside of Chimera to get different charges. If so, somebody else will have to answer the scripting part of your question! Best Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Feb 1, 2008, at 9:47 AM, snoze pa wrote:
Dear Chimera Users, How can I use chimera in --nogui mode to screen 1000 compunds from ZINC database and save them in to mol2 format. Is there any script so that I can convert preselected 1000 compound from ZINC database and convert them t o mol2 format so that I can use them in DOCK program. thanks in advance