Dear all:
When I used ptraj to get bfactors from my trajectory file, the ptraj.in
file is like this:
trajin npt.mdcrd
rms first out zb.b :1-298.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
only more than 70 B-factors, which should be 298, in the bfactor.out
file. I examined the calculation progress also, and it is like this:
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.CA
Mask [:1-298.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
zb.b
Atom selection follows
:1.CA,:6.CA,:10.CA,:16.CA,:17.CA,:21,CA,:22.CA,:26.CA,:31,CA,:32.CA
:36.CA,:40.CA,:46,CA,:47.CA,:47.CA,:51,CA,:52.CA,:56.CA,:66.CA,:70.CA
:75.CA,:80.CA,:85.CA,:88.CA,:93.CA,:95.CA,:100.CA,:105.CA,:109.CA,:115.C
A
:119.CA,:124.CA,:128,CA,:129.CA,:133.CA,:138,CA,:139.CA,:149,CA,:150.CA,
:155,CA
:156.CA,:159.CA,:165.CA,:169.CA,:173,CA,:174.CA,:178,CA,:179.CA,:179.CA,
:184.CA
:184.CA,:189.CA,:195.CA,:200.CA,:204.CA,:210.CA,:215.CA,:219.CA,:225.CA,
:230.CA
:236.CA,:245.CA,:250.CA,:255.CA,:260.CA,:266.CA,:269.CA,:271.CA,:274,CA,
:275.CA
:280,CA,:281.CA,:285,CA,:286.CA,:291.CA,:296.CA
7> ATOMICFLUCT: dumping B factors by atom to file bfactor.out
Atom selection
:1.CA,:6.CA,:10.CA,:16.CA,:17.CA,:21,CA,:22.CA,:26.CA,:31,CA,:32.CA
:36.CA,:40.CA,:46,CA,:47.CA,:47.CA,:51,CA,:52.CA,:56.CA,:66.CA,:70.CA
:75.CA,:80.CA,:85.CA,:88.CA,:93.CA,:95.CA,:100.CA,:105.CA,:109.CA,:115.C
A
:119.CA,:124.CA,:128,CA,:129.CA,:133.CA,:138,CA,:139.CA,:149,CA,:150.CA,
:155,CA
:156.CA,:159.CA,:165.CA,:169.CA,:173,CA,:174.CA,:178,CA,:179.CA,:179.CA,
:184.CA
:184.CA,:189.CA,:195.CA,:200.CA,:204.CA,:210.CA,:215.CA,:219.CA,:225.CA,
:230.CA
:236.CA,:245.CA,:250.CA,:255.CA,:260.CA,:266.CA,:269.CA,:271.CA,:274,CA,
:275.CA
:280,CA,:281.CA,:285,CA,:286.CA,:291.CA,:296.CA,:307.CA
I have tried what I could try, but still got the same results. Now, I
turn to you, any help from you will be greatly appreciated!
Regards,
Zhang Bing
NUSNNI
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Thu Sep 01 2005 - 08:53:01 PDT
