[Chimera-users] scan and minimization of dihedral angle

Elaine Meng meng at cgl.ucsf.edu
Mon Aug 25 09:30:40 PDT 2014

On Aug 24, 2014, at 2:04 PM, Milo Westler <milo at 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.

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 C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

-------------- next part --------------
A non-text attachment was scrubbed...
Name: lig.prmtop
Type: application/octet-stream
Size: 7900 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20140825/8d53d822/attachment.obj>
-------------- next part --------------

More information about the Chimera-users mailing list