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AMBER Archive (2005)Subject: AMBER: ptraj problem
From: Zhang Bing (nnizb_at_nus.edu.sg)
Dear all:
When I used ptraj to get bfactors from my trajectory file, the ptraj.in
trajin npt.mdcrd
rms first out zb.b :1-298_at_CA
atomicfluct out bfactor.out @CA byatom bfactor
after I issued: ptraj my.prmtop ptraj.in
the calculation can be done smoothly, however, I noticed that there is
Initializing state: detected PBC beta angle in prmtop that is not 90.0!
Assuming this box is a truncated octahedron, angle is 109.471221
PTRAJ: Processing input file...
Input is from file bfact.in
PTRAJ: trajin npt.mdcrd
Checking coordinates: npt.mdcrd
PTRAJ: rms first out zb.b :1-298_at_CA
Mask [:1-298_at_CA] represents 76 atoms
PTRAJ: atomicfluct out bfactor.out @CA byatom bfactor
Mask [@CA] represents 77 atoms
FYI: No output trajectory specified (trajout), none will be saved.
PTRAJ: Successfully read the input file.
Coordinate processing will occur on 1000 frames.
Summary of I/O and actions follows:
INPUT COORDINATE FILES
File (npt.mdcrd) is an AMBER trajectory (with box info) with 1000 sets
OUTPUT COORDINATE FILE
NULL entry
ACTIONS
1> RMS to first frame using no mass weighting
Dumping RMSd vs. time (with time interval 1.00) to a file named
Atom selection follows
:280,CA,:281_at_CA,:285,CA,:286_at_CA,:291_at_CA,:296_at_CA
7> ATOMICFLUCT: dumping B factors by atom to file bfactor.out
Atom selection
:280,CA,:281_at_CA,:285,CA,:286_at_CA,:291_at_CA,:296_at_CA,:307_at_CA
I have tried what I could try, but still got the same results. Now, I
Regards,
Zhang Bing
NUSNNI
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