Hi
On Fri, May 20, 2016 at 3:58 PM, Arati Paudyal <apsilwal123.gmail.com>
wrote:
> Hi Hai,
>
> thank you for your reply. could you please give a little bit more detail on
> the how to properly use 'autoimage". Do you basically go to cpptraj and
> type autoimage? what would be the proper steps and command to run to
> autoimage?
Please follow this cpptraj's tutorial:
http://www.amber.utah.edu/AMBER-workshop/London-2015/DNA-tutorial/
(Just need to read section: *Analysis of the trajectory using CPPTRAJ*).
in short, below is cpptraj command.
parm your.parm7
trajin your.nc
autoimage
trajout your.autoimage.nc
Then do anything with `your.autoimage.nc`
> After reading some of the answers from Ambermailing list I am
> scared that I might messed up the original structure or something. I looked
> up the manual and I am still not clear. If you could guide be through some
> steps I would really appreciate it.
>
Try above tutorial, generate new trajectory after doing autoimage, viewing
it in VMD.
> Also, does that affect my analysis and calculation (like alanine scanning,
> decomposition etc)? Or this is simply for the viewing purpose?
>
>
It does. For example if you simulation DNA duplex with PBC, you might see
its strands fall far apart.
You will get very high value if computing thinks link RMSD to B-form, or
distance between base pair in two strands.
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Received on Fri May 20 2016 - 14:00:03 PDT
