Dear Amber users!
I've faced with some problems during processing of the trajectories using
ptraj (I'm dealing with the simulation of membrane embedded protein using
amber12 + amber -tools -12 for the analysing)
1) need to remove periodicity and wrapping from my trajectory
trajin md.nc 1000 last 5
reference protein.inpcrd
unwrap
center :1-289 mass origin
image origin center
# write new trajectory
trajout md_proc.nc netcdf nobox
rms reference :1-289.CA out rmsd.dat
outtraj afterRMSD.nc
using the above inpuit file my trajectory seems OK but water constantly
diffuse from and to the boundaries of the system.
if I remove 'unwrap' that the no problem with water but my system wrapping
along the Z direction.
2) if I chose possibility to save trajectory after RMSD fitting
trajin md.nc 1000 last 5
reference protein.inpcrd
rms reference :1-289.CA out rmsd.dat
outtraj afterRMSD.nc
it has produced correct RMSD.dat output but no any processed trajectory
afterRMSD.nc has been appeared in the work dir.
Thanks for help,
James
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Received on Mon Sep 08 2014 - 02:00:02 PDT
