Dear Ross walker,
Thank you very much for your reply and suggestions. I did superimposed a
reference pdb file (which i have used as a reference while calculating the
rms deviation) and a .crd file into vmd. It is loading all the frames of
md5.crd (this is the file with which I have the problem while calculating
rmsd using ptraj). Then I calculated the rms deviation using vmd tcl script
it is running well and giving the rmsd (the rmsd appears to be reasonable).
The output file md5.crd appears to be as good as other crd files.
Thank you very much.
Ram.
On Feb 8, 2008 10:10 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> 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
>
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> be read every day, and should not be used for urgent or sensitive issues.
>
>
> ------------------------------
> *From:* owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] *On
> Behalf Of *rams rams
> *Sent:* Thursday, February 07, 2008 21:36
> *To:* amber.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.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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Received on Wed Feb 13 2008 - 06:07:14 PST
