Dear Dr. Adrian and Aron,
Thank you very much for your reply. My senior showed me how to
get all these pdb from the crd files from the simulations using the perl
script. Actually, there was nothing wrong in my prmtop files. In fact, I
was trying to get these pdb without using the perl scipt.
Thanks for help,
Mahendra Thapa
On Mon, Feb 20, 2012 at 4:09 PM, Thapa, Mahendra (thapamb) <
thapamb.mail.uc.edu> wrote:
>
>
>
> ________________________________________
> From: Adrian Roitberg
> Sent: Monday, February 20, 2012 3:09:16 PM (UTC-06:00) Central America
> To: AMBER Mailing List
> Subject: Re: [AMBER] problem in getting required snapshots
>
> 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
>
>
>
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Received on Fri Feb 24 2012 - 09:30:03 PST
