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 Mon Feb 20 2012 - 13:30:02 PST
