Hello amber users,
I am working on 2 variants (wild-type and mutant) of a hexameric protein (a
trimer of dimer) and would like to perform an RMS fitting (using just
C-alpha atoms) of the trajectories generated for the 2 systems. Sadly, due
to the underlying symmetry in the protein, when I try to align the 2
different trajectories and save the new RMS fit trajectory (only CA atoms),
I end up getting a flip in the protein conformation at the concatenation.
In other words, The prod_*wt*_imaged_CA.nc and prod_*mt*_imaged_CA.nc
trajectories are flipped. Below is the script I used. Could anyone please
help me with this? I was also wondering if 'srmsd' (symmetry corrected
rmsd) is available for RMS fitting so that I can use that and save the
trajectory which could also solve the problem. I need this RMS fit
concatenated trajectory for clustering (which I do with srmsd) and PCA
analysis (to have the projections on the same eigen space)
parm wt_CA.prmtop
trajin prod_wt_imaged_CA.nc
trajin prod_mt_imaged_CA.nc
center :1-160 mass origin
image origin center familiar
center :1-321 mass origin
image origin center familiar
center :1-481 mass origin
image origin center familiar
center :1-642 mass origin
image origin center familiar
center :1-802 mass origin
image origin center familiar
center :1-963 mass origin
image origin center familiar
reference wt_CA.pdb [init]
rms :1-963 ref [init] mass
trajout wt_mt_combined-CA-RMSfit.nc
run
quit
Thank you
Venkat
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Received on Mon Oct 14 2019 - 07:00:02 PDT
