On Aug 24, 2014, at 2:04 PM, Milo Westler <milo@nmrfam.wisc.edu> wrote:

> I also sent a second message asking how to write out the parameters determined from antechamber. (write prmtop doesn't work for me)

Hi Milo,
I didn't see this other message (but maybe it hasn't come through for some reason), but I was able to use Write Prmtop on the ligand.pdb file you sent, in both Chimera 1.9 and the current pre-1.10 daily build.  The result from Chimera 1.9 is attached.  The files differed only very slightly, could have been rounding.

You should use at least Chimera 1.9, as there was a Write Prmtop bugfix in that version.
<http://www.rbvi.ucsf.edu/chimera/docs/relnotes/1.9.html>

If you are using Chimera 1.9 or newer, but still get an error of some kind, you could report the bug (menu: Help… Report a Bug).  Thanks!
Elaine
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Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco