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,
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trajin input.mdcrd
rms first mass out output.rms time 5
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Following is the excerpt from the output;
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...
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�)...
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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.
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Received on Wed Aug 06 2008 - 06:07:21 PDT
