Hi Josh, I believe a newer version of Chimera will solve this problem. Get snapshot version 1.2255: http://www.cgl.ucsf.edu/chimera/download.html#snapshots Chimera version 1.2255 includes Antechamber and calls it automatically from Dock Prep. In version 1.2199, Dock Prep only added charges to standard residues, as the procedure for nonstandard residues was still under development. Best, Elaine On Jun 28, 2006, at 1:50 PM, Joshua D Campbell wrote:

Hello, My name is Josh Campbell and I'm trying to prepare a ligand for docking that is made up of non-standard residues using Chimera. The Dock Prep tool of course does not assign charges to non-standard atoms. I looked at your UserGuide and it said that there were other places to calculate non-standard residues using the Antechamber module, but I could not find any of these tools anywhere in the Chimera program. If you could give me some clarification as to adding charges on non-standard residues, I would be very greatful. I am working with "beta version 1 build 2199 2006/01/24". Thanks.

Sincerely, Josh Campbell Harvard Medical School Laboratory of Structural Cell Biology _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

----- 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