Elaine, I guess i can use either 'minimize' or "addh and addcharge" otherwise it will run the antechamber twice. *minimize is working fine but i can not save the result in mol2 format using COMMAND option. I try wrtiemol2 but it is not accepting it as a command. save is also not saving in mol2 format. *Any help, thanks in advance. s * * On Wed, Feb 27, 2008 at 5:48 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:

Hi Conrad, From looking at the documentation, sounds like you can't use the minimize command with any nondefault settings of Dock Prep, addh, and add charge. Is that correct?

It would be nice if it could tell that you already added hydrogens and charges to your liking and skip those steps. However, since this is all done via Dock Prep, that may or may not be possible. 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