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
> _______________________________________________
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> 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
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Received on Mon Feb 20 2012 - 13:30:02 PST
