I'm not clear on this whole compressed versus uncompressed thing. It looks
like your input is an uncompressed file, but all your messages refer to a
.gz, which would be an archive. Did you rename your file to have .gz at
the end in order to run that script? That seems odd.
Also as mentioned in the last reply, do the PDBs you got look ok? If those
PDBs look fine then I would say the script is ok, and your file is not.
In the case that it is your file, I would look into the following things:
1) Are you certain (from the mdout file for instance) that the simulation
actually finished? It could be that it crashed after 281 frames.
2) Similar to #1, can you check using a very quick simulation what the size
of say a 10-frame file is, and make sure that your file size matches what
you would expect for 5000-frames? It could be that some information has
been lost from your file.
3) Can you try opening it in VMD instead and see if the same error persists?
4) Are you transferring the file from another machine in order to analyze
it, is it possible that some damage occurs to the file during transfer?
~Aron
On Mon, Feb 20, 2012 at 4:09 PM, Adrian Roitberg <roitberg.ufl.edu> wrote:
> did you try uncompressing the file yourself and changing the ptraj
> script to :
>
> trajin equil1.mdcrd 1 5000 1
> trajout equil1.pdb.pdb
>
>
> ?
>
> that should tell you if the file is truly compressed or not.
>
> Also, are you positive that the prmtop is the correct one?
>
> lastly, did you look at pdb it DID create to see if they are what you
> expect?
>
> On 2/20/12 4:05 PM, Mahendra B Thapa wrote:
> > Dear Amber Users,
> >
> > I run 5ns MD simulation using
> > amber11 with nstlim = 2500000, dt = 0.002 ps, ntpr = 100, ntwr = 500 and
> > ntwx = 500; I then got equil1.crd as the coordinate file. The total
> number
> > of snapshots will be 5000. To get all 5000 snapshots as pdb, I issued the
> > following command:
> > ptraj prmtop<script>& ptraj1.out
> > where, script ( I called it ptraj1.in) read as
> > trajin equil1.mdcrd.gz 1 5000 1 [ I
> > changed coordinate file equil1.crd in equill1.mdcrd.gz ]
> > trajout equil1.pdb pdb
> >
> > But, I got only 281 frames(instead of 5000) with the following message in
> > the output body [ ptraj1.out ] :
> >
> > checkCoordinates(): Could not predict number of frames for AMBER
> trajectory
> > file: equil1.mdcrd.gz
> > If this is not a compressed file then there is a problem
> > Rank: 0 Atoms: 21770 FrameSize: 529011 TitleSize: 81 NumBox: 0 Seekable 0
> > FYI ptrajSetupIO(): trajin stop value (5000) is greater than the number
> of
> > sets read in.
> > Setting stop to the maximum value (281)
> > PTRAJ: trajout equil1.pdb pdb
> > equil1.mdcrd.gz: 281 frames.
> > PTRAJ: Successfully read the input file.
> > Coordinate processing will occur on 281 frames.
> > Summary of I/O and actions follows:
> >
> > INPUT COORDINATE FILES
> > File (equil1.mdcrd.gz) is an AMBER trajectory with 281 sets
> >
> > OUTPUT COORDINATE FILE
> > File (equil1.pdb) is a PDB file
> >
> > NO ACTIONS WERE SPECIFIED
> >
> >
> > Let me help where I did the mistakes; I just tried to follow the tutorial
> > B1,section 3.
> >
> > Thanks,
> > Mahendra Thapa
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> Dr. Adrian E. Roitberg
> Professor
> Quantum Theory Project, Department of Chemistry
> University of Florida
> roitberg.ufl.edu
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Feb 20 2012 - 13:30:02 PST
