Hi Snoze, The command for saving coordinates is "write", see http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/write.html You will also want to use the "format mol2" option, and perhaps other options described on that page. 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 27, 2008, at 4:04 PM, snoze pa wrote:
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