[Chimera-users] minimize command

snoze pa snoze.pa at gmail.com
Wed Feb 27 16:04:37 PST 2008

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.
On Wed, Feb 27, 2008 at 5:48 PM, Elaine Meng <meng at 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 at 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
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