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
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
participants (2)
-
Elaine Meng -
snoze pa