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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Received on Sun Nov 10 2024 - 21:00:01 PST
