AMBER Archive (2008)

Subject: RE: AMBER: WARNING in readAmberTrajectory(): fsetpos() failed on when looking for box coordinates!

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Fri Feb 08 2008 - 10:40:25 CST

Hi Ram,
 
This likely means that the md5.crd file is corrupt - this can happen
occasionally due to hardware failures - particularly if you are running on a
home built cluster that uses NFS mounts for the data drives. There really is
not a great deal you can do here. You could take a look at the trajectory
file and try to work out which piece is corrupt. Can you load it into
something like vmd okay? Does the output that goes with md5.crd look good?
Or did the job crash before completion?
 
Your best approach will likely be to just rerun step 5 of your simulation
using the restart file from step 4. This is why I tend to break up my
simulations in small chunks (of around 6 to 12 hours run time each) and save
the restarts in between. Thus if something gets corrupted you can rerun the
gap in the middle to generate the trajectory.
 
The big problem with the ASCII crd files is if one frame gets corrupted, say
a short write, it breaks the entire file since there is no record
information in there. With the binary netcdf file format I believe that if
one frame gets corrupted you can just ignore that frame and still process
the rest of the file - I'm not sure how well this works in practice however,
maybe others can chime in here.
 
I'm sorry I can't help much more.
 
All the best
Ross
 

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From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
rams rams
Sent: Thursday, February 07, 2008 21:36
To: amber_at_scripps.edu
Subject: AMBER: WARNING in readAmberTrajectory(): fsetpos() failed on when
looking for box coordinates!

Dear Amber users,

I have come across the following warning message while calculating the rms
deviations using ptraj:

The input I am using is the following:

trajin md1.crd
trajin md2.crd
trajin md3.crd
trajin md4.crd
trajin md5.crd

reference min1.pdb
rms reference out rmsd_all.dat :1-299_at_CA

while processing the data, on the screen the following message appeared:

WARNING in readAmberTrajectory(): fsetpos() failed on when looking for box
coordinates!

This is the case only if I include the trajin md5.crd file. With the first
four crd files it went well. Also I noticed that, the file sizes of all
first four crd files are the same (229296 blocks) where as the 5th one is
having 232128 blocks despite of the fact that all the crd files are having
the same 250 ps information.

The out file is having the folliwng:

Processing AMBER trajectory file md4.crd

Set 1 .................................................
Set 50 .................................................
Set 100 .................................................
Set 150 .................................................
Set 200 .................................................
Set 250
Processing AMBER trajectory file md5.crd

PTRAJ: Successfully read in 1000 sets and processed 1000 sets.
       Dumping accumulated results (if any)

PTRAJ RMS: dumping RMSd vs time data

Can clearly find something wrong with the md5.crd file.

The data file its generating looks like this:

 995.00 1.23954
  996.00 1.21150
  997.00 1.22010
  998.00 1.20672
  999.00 1.20813
 1000.00 1.24189
 1001.00 0.00000
 1002.00 0.00000
 1003.00 0.00000
 1004.00 0.00000
 1005.00 0.00000
 1006.00 0.00000
 1007.00 0.00000
 1008.00 0.00000

Part of it I have given here. Upto 1000, it is the information about the
first 4 crd files. From 1001 to 1250 it is displaying only zeros.

Can any one help me in looking at these details more carefully.

Thanks and Regards,
Ram.

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