AMBER Archive (2005)

Subject: AMBER: ptraj problem

From: Zhang Bing (nnizb_at_nus.edu.sg)
Date: Thu Sep 01 2005 - 02:01:20 CDT


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_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
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_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
zb.b

      Atom selection follows
:1_at_CA,:6_at_CA,:10_at_CA,:16_at_CA,:17_at_CA,:21,CA,:22_at_CA,:26_at_CA,:31,CA,:32_at_CA

 
:36_at_CA,:40_at_CA,:46,CA,:47_at_CA,:47_at_CA,:51,CA,:52_at_CA,:56_at_CA,:66_at_CA,:70_at_CA

 
:75_at_CA,:80_at_CA,:85_at_CA,:88_at_CA,:93_at_CA,:95_at_CA,:100_at_CA,:105_at_CA,:109_at_CA,:115_at_C
A

 
:119_at_CA,:124_at_CA,:128,CA,:129_at_CA,:133_at_CA,:138,CA,:139_at_CA,:149,CA,:150_at_CA,
:155,CA

 
:156_at_CA,:159_at_CA,:165_at_CA,:169_at_CA,:173,CA,:174_at_CA,:178,CA,:179_at_CA,:179_at_CA,
:184_at_CA

 
:184_at_CA,:189_at_CA,:195_at_CA,:200_at_CA,:204_at_CA,:210_at_CA,:215_at_CA,:219_at_CA,:225_at_CA,
:230_at_CA

 
:236_at_CA,:245_at_CA,:250_at_CA,:255_at_CA,:260_at_CA,:266_at_CA,:269_at_CA,:271_at_CA,:274,CA,
:275_at_CA

    :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
:1_at_CA,:6_at_CA,:10_at_CA,:16_at_CA,:17_at_CA,:21,CA,:22_at_CA,:26_at_CA,:31,CA,:32_at_CA

 
:36_at_CA,:40_at_CA,:46,CA,:47_at_CA,:47_at_CA,:51,CA,:52_at_CA,:56_at_CA,:66_at_CA,:70_at_CA

 
:75_at_CA,:80_at_CA,:85_at_CA,:88_at_CA,:93_at_CA,:95_at_CA,:100_at_CA,:105_at_CA,:109_at_CA,:115_at_C
A

 
:119_at_CA,:124_at_CA,:128,CA,:129_at_CA,:133_at_CA,:138,CA,:139_at_CA,:149,CA,:150_at_CA,
:155,CA

 
:156_at_CA,:159_at_CA,:165_at_CA,:169_at_CA,:173,CA,:174_at_CA,:178,CA,:179_at_CA,:179_at_CA,
:184_at_CA

 
:184_at_CA,:189_at_CA,:195_at_CA,:200_at_CA,:204_at_CA,:210_at_CA,:215_at_CA,:219_at_CA,:225_at_CA,
:230_at_CA

 
:236_at_CA,:245_at_CA,:250_at_CA,:255_at_CA,:260_at_CA,:266_at_CA,:269_at_CA,:271_at_CA,:274,CA,
:275_at_CA

: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
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_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu