Dear all,
There are some topics about generating average structures from mdcrd
trajectory files but how can we do starting from rst or pdb NMR
structures. It must be possible as evocated in the section 6 of the
tutorial 3.
I have first tried to trajin all my rst but it seems that only the first
file is taken in account:
trajin xca_1.rst
trajin xca_2.rst
...
...
rms first mass out all.fit .N1,C9,C11,N2,C12,C17,C20,N3,C21,C29,N4
image center familiar
STRIP :CL3
average average.pdb pdb nowrap
So in a second stage, I have concatenated with the cat command and then
launch the my traj script:
trajin xca_all.rst
rms first mass out all.fit .N1,C9,C11,N2,C12,C17,C20,N3,C21,C29,N4
image center familiar
STRIP :CL3
average average.pdb pdb nowrap
But in this case, I have this error message:
PTRAJ: Processing input from "STDIN" ...
PTRAJ: trajin all.rst
Checking coordinates: all.rst
readAmberRestart(): topology/coordinates file are inconsist with
NATOMS = 1138 (1248)
PTRAJ: rms first mass out all.fit .N1,C9,C11,N2,C12,C17,C20,N3,C21,C29,N4
Mask [.N1,C9,C11,N2,C12,C17,C20,N3,C21,C29,N4] represents 11 atoms
PTRAJ: image center familiar
Mask [*] represents 1248 atoms
PTRAJ: STRIP :CL3
Mask [:CL3] represents 1165 atoms
PTRAJ: average average.pdb pdb nowrap
Mask [*] represents 83 atoms
WARNING in ptraj(): No input trajectories specified (trajin), aborting...
What is the best way to do that? thanks
Best regards,
Baptiste
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Received on Thu Mar 03 2011 - 09:30:04 PST
