Hi,
I have been trying to run a CPPTRAJ script to generate a trajectory with just CA atoms using the following script:
parm <name>.prmtop
trajin nowaters/<name>_nowaters.nc
autoimage
rms first .CA
average crdset AVG
run
rms ref AVG .CA
# strip and output results.
strip !.CA outprefix CA
trajout CA_traj/<name>_CA.nc
run
clear all
However this was resulting in output trajectories where the X, Y and Z co-ordinates were sometimes in the wrong column as demonstrated by residues 127-131 in this section of a pdb file :
ATOM 123 CA GLN 123 68.309 29.110 1.473 1.00 0.00 C
ATOM 124 CA LEU 124 66.353 31.970 -0.226 1.00 0.00 C
ATOM 125 CA ARG 125 67.566 34.771 -2.529 1.00 0.00 C
ATOM 126 CA ASP 126 67.312 38.488 -2.652 1.00 0.00 C
ATOM 127 CA SER 127 35.179 -2.383 68.197 1.00 0.00 C
ATOM 128 CA LYS 128 37.592 0.697 68.026 1.00 0.00 C
ATOM 129 CA SER 129 40.316 -1.856 66.986 1.00 0.00 C
ATOM 130 CA SER 130 11.099 79.441 67.583 1.00 0.00 C
ATOM 131 CA ASP 131 14.290 80.687 69.232 1.00 0.00 C
ATOM 132 CA LYS 132 72.574 38.092 -1.012 1.00 0.00 C
ATOM 133 CA SER 133 70.558 35.313 0.680 1.00 0.00 C
ATOM 134 CA VAL 134 68.398 34.435 3.699 1.00 0.00 C
I have not been able to figure out what has caused this – but thought there may be an issue in CPPTRAJ?
Many thanks,
Annabelle
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Received on Fri Sep 24 2021 - 08:00:03 PDT
