Hi,
What version of AmberTools are you using? If you are using 1.5, have
you applied all of the bugfixes (
http://ambermd.org/bugfixesat.html)?
There was a bug that affected large gzipped trajectory files that has
since been fixed.
-Dan
On Mon, Feb 20, 2012 at 4:05 PM, Mahendra B Thapa <thapamb.mail.uc.edu> 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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Received on Tue Feb 21 2012 - 04:30:01 PST
