Re: [AMBER] Reorienting the protein during simulation

From: Ahmed Mashaly <>
Date: Wed, 17 Jan 2018 10:39:01 +0000 (UTC)

Dear Dan
Thanks for the quick answer.
The box fits very well if the protein is aligned to the main axis, the problem happens after it rotates 90 degrees (it is a very tall protein, so it exceeds the box sides when it is rotated) and one side may interact with the other side in case of periodic conditions.
Another problem is that we are expecting a change in conformation, so we don't want to apply restraints, other solution is to increase the box size from 14 Angstrom to 20 which will take double of simulation time. So before moving to this step I want to make sure that there is no other solution through cpptraj actions? Kind Regards,Ahmed

      From: Daniel Roe <>
 To: AMBER Mailing List <>
 Sent: Tuesday, January 16, 2018 3:54 PM
 Subject: Re: [AMBER] Reorienting the protein during simulation

The important thing to remember is that with periodic boundary
conditions your protein is *never* really outside the box. It may
appear to be outside the boundaries of your unit cell, but it is
always interacting with its images. If your protein is rotating so
that it is no longer aligned with your unit cell axes it is because it
is favorable to do so. Your box may be too small. If you absolutely
need the protein to remain aligned with e.g. the Z axis you'll
probably have to apply some external restraint and make sure you
correct for it in any later analysis if necessary.

On Tue, Jan 16, 2018 at 5:52 AM, Ahmed Mashaly <> wrote:
> This is what I use for recentering>
> trajin my_rst_file.r>
> autoimage
> center: 1-1500 mass origin>
> image origin center

The 'center' and 'image' commands in this case will override whatever
was done with 'autoimage', so it's not useful to combine the two.
Either use 'autoimage' (recommended) *or* use 'image'/'center'.

> I also tried to add>
> prinicipal :1-1500 dorotation mass

Note that the rotation done by 'principal' means that further imaging
after this will not be possible.


Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
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Received on Wed Jan 17 2018 - 03:00:02 PST
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