As far as I know these can be ignored. The rms fitting rotates the box
vectors in each frame out of alignment with the cartesian coordinate
vectors, so the resulting frames could not be used as starting points for
another MD simulation or stored in a format that expects a,b,c to be
colinear with x,y,z. If you want the rms fit to be done, there is no way
(or need) to fix it. For analysis of your simulation the misaligned boxes
likely wont matter.
OTOH, if my understanding here is wrong I'll be very happy if someone on
the list can point this out :-)
Kind Regards.
Thomas
On Mon, Nov 11, 2024 at 5:45 AM Guberman-Pfeffer, Matthew via AMBER <
amber.ambermd.org> wrote:
> **Warning** The sender address ("Guberman-Pfeffer, Matthew via AMBER" )
> can not be verified, sender email address could be spoofed. Please take
> care to proceed.
> Dear Amber Community,
>
> I want to center a trajectory on a specific residue, perform RMS fitting,
> and save the resulting trajectory. Is the below cpptraj script correct?
>
>
> parm r1280.prmtop
>
> trajin prod_1.mdcrd 1 last 1
>
> trajin prod_2.mdcrd 1 last 1
>
> ttrajin prod_1280centered.nc 1 last 1
>
>
> unwrap ^1
>
> center :HEH&:1280 mass origin
>
> image origin center
>
>
> rms name :1-1321&@N,CA,C,O&!.H=&!:WAT,PRN first out rmsd.dat mass
>
>
> trajout prod_1280rms.nc
>
>
> run
>
> Note, when I use this script on a simulation I previously saved without
> the rms command (but using all the others in the script), I get:
> I’m getting the following warning when I load into cpptraj a trajectory I
> previously wrote with cpptraj:
>
> Warning: Set 1; unit cell is not X-aligned. Box cannot be properly stored
> as Amber NetCDF trajectory.
>
> And so on for every frame.
>
> How can I fix this issue?
>
> Best,
> Matthew
>
>
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
*Dr. Thomas Steinbrecher*
Principal Scientist CADD
Roche Pharma Research and Early Development
Roche Innovation Center Basel
F. Hoffmann-La Roche Ltd
Bldg. 06/OG07
Grenzacherstrasse 124
4070 Basel
Switzerland
Phone +41 61 682 1319
mailto: thomas.steinbrecher.roche.com
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Received on Sun Nov 10 2024 - 23:30:02 PST
