Hi,
There was nothing attached to your email so I'll just give some general advice.
First, I'm not sure what version of cpptraj you are using, but it's
usually better to use the latest version from AmberTools or even
better yet from GitHub: https://github.com/Amber-MD/cpptraj
Second, could you post the exact cpptraj inputs you have tried?
Third, if you would like please send me off-list topology and
coordinates I can use to try and reproduce your problem.
Hope this helps,
-Dan
On Wed, Apr 6, 2022 at 9:57 AM Boris Gomaz <boris.gomaz.irb.hr> wrote:
>
> To whom it may concern,
>
> I have some issues with centering the protein structure in my simulation
> box. The protein is hexameric and my box is a truncated octahedron.
> During 1 microsecond of the simulation, protein wonders out of the box.
> After the simulation, I calculated the RMSD and it looks like this:
>
> Then I used autoimage from cpptraj, and after RMSD calculation I got
> something like this:
>
> I tried various different combinations, with anchoring to the origin,
> with anchoring all the amino acids, and the result is the same. I also
> tried centering on different structures, and the results are the same.
> Do you have any suggestions on how to fix this problem or is this
> something that already occurred as a problem?
>
> Thank you in advance for your answer,
>
> --
> Boris Gomaz
>
> Laboratory for chemical and biological crystallography
> Division of Physical Chemistry
> Ruđer Bošković Institute
> Bijenička cesta 54, 10000 Zagreb
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Apr 06 2022 - 07:30:02 PDT
