Hi,
The 'autoimage' command is only available in a fully updated
AmberTools12 version of cpptraj.
-Dan
On Fri, Feb 8, 2013 at 9:35 PM, Jonathan Saboury <jsabou1.gmail.com> wrote:
> After about a 720 picosecond simulation of a prmtop and inpcrd file created
> by AMBER from a pdb created in spartan '08 in OpenMM I get a pdb file
> showing the simulation that is visualized with VMD.
>
> At 360 picoseconds teh molecule seems to go out of the box of water and I
> was told it was an imaging issue and to use autoimage in cpptraj to
> restructure to output the simulation correctly.
>
> When I try to run autoimage I get "Warning: Unknown Command autoimage."
>
> Here is the commands to get the prmtop and inpcrd files:
> http://pastebin.com/raw.php?i=63sFFQ6q
>
> and here are the commands i tried to run autoimage (outputPyMol.pdb is the
> file created by OpenMM): http://pastebin.com/raw.php?i=6R9VNvFp
>
>
> Thank you for your time, it is very much appreciated!
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Fri Feb 08 2013 - 21:00:03 PST
