Re: [AMBER] Protein moving out of the water box

From: Hai Nguyen <>
Date: Fri, 20 May 2016 16:37:18 -0400


On Fri, May 20, 2016 at 3:58 PM, Arati Paudyal <>

> 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:
(Just need to read section: *Analysis of the trajectory using CPPTRAJ*).

in short, below is cpptraj command.

parm your.parm7

Then do anything with ``

> 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
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