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

From: Arati Paudyal <>
Date: Fri, 20 May 2016 20:21:33 -0400


thank you again for your reply. That tutorial was really helpful.
So I did the autoimage and visualized the protein in VMD with no luck. I
didn't even see any difference before and after autoimage. So I guess I am
stuck with this simulation.

I have run the same simulation before for 60 ns BUT with iwrap. It was fine
and the protein stayed inside water boundary. With iwrap the waterbox looks
really good rectangular shape and I guess the image quality is also better
but now this problem.

My protein complex looked ok and they stayed intact for the entire
simulation. The protein-protein interaction part always remained inside the
water boundary . The part that is moving in-out of the boundary is a small
C-terminal tail that is just dangling. I compared my data from 60 ns and 80
ns (with iwrap) and they are very close. SO I don't think that mattered a

Do you suggest running simulation again without iwrap? I need to publish
this data and I don't want any doubts on the simulation part. Please
suggest anything!


On Fri, May 20, 2016 at 4:37 PM, Hai Nguyen <> wrote:

> Hi
> On Fri, May 20, 2016 at 3:58 PM, Arati Paudyal <>
> 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:
> (Just need to read section: *Analysis of the trajectory using CPPTRAJ*).
> in short, below is cpptraj command.
> parm your.parm7
> trajin
> autoimage
> trajout
> 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 - 17:30:04 PDT
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