AMBER Archive (2008)

Subject: AMBER: Set 251 is corrupted, ptraj error...

From: Waqas Nasir (nasirwaqas1983_at_yahoo.com)
Date: Mon Aug 04 2008 - 09:54:09 CDT

Hi,

Hope everyone is doing fine.

I am using amber version 8 and trying to get the rms plot for my md run of length 500ps. I use the following simple script to get the rms file,
-----------------------------------------------------------------------------------------------------------------------------------
trajin input.mdcrd
rms first mass out output.rms time 5
-----------------------------------------------------------------------------------------------------------------------------------

Following is the excerpt from the output;

-----------------------------------------------------------------------------------------------------------------------------------
...
PTRAJ: Processing input file...
       Input is from standard input

PTRAJ: trajin input.mdcrd
Checking coordinates: input.mdcrd

PTRAJ: rms first mass out output.rms time 5
Mask [*] represents 9438 atoms
FYI: No output trajectory specified (trajout), none will be saved.

PTRAJ: Successfully read the input file.
       Coordinate processing will occur on 250 frames.
       Summary of I/O and actions follows:

INPUT COORDINATE FILES
  File (input.mdcrd) is an AMBER trajectory with 250 sets

OUTPUT COORDINATE FILE
  NULL entry

ACTIONS
  1>  RMS to first frame using mass weighting
      Dumping RMSd vs. time (with time interval 5.00) to a file named output.rms
      Atom selection follows   * (All atoms are selected)

Processing AMBER trajectory file input.mdcrd

Set      1 .................................................
Set     50 .................................................
Set    100 .................................................
Set    150 .................................................
Set    200 .................................................
Set    250
ERROR in readAmberTrajectory(): Set #251 is corrupted (
(� X5P\H��N�)...

------------------------------------------------------------------------------------------------------------------------------------

Now, I dont know in the first place what these "sets" represent. How many atoms or coordinates are there in one set. Because to track the error I must know the position of the set where the error actually is. My mdcrd file is more than 700000 lines, so I cant figure that out manually.

Any help in this regard will be highly appreciated.

Regards,
Waqas

PS: I chekced with my input.mdcrd file and its less than 4GB.

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu