Hi Pete,
I tried to gzip it, but it won't process. I suspect that the errors might come from my trajectory file itself - still identifying why.
Thanks for the suggestion
________________________________
From: "Gannett, Peter" <pgannett.hsc.wvu.edu>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Wednesday, September 26, 2012 8:34 AM
Subject: Re: [AMBER] Could not open mdcrd file with mode (r)
On occasion this has happened to me and always when the mdcrd file was very large. I found that if I gzipped it, the file could be read. I know this does not make sense, but, then again, by doing this, I could process the trajectory....
Pete
________________________________________
From: Bill Ross [ross.cgl.ucsf.EDU]
Sent: Tuesday, September 25, 2012 7:56 PM
To: amber.ambermd.org
Subject: Re: [AMBER] Could not open mdcrd file with mode (r)
> If permission is still denied,
Note that there was no permission denied error reported, just a failure
to open with read permission.
Bill
Jason Swails <jason.swails.gmail.com> wrote:
> On Tue, Sep 25, 2012 at 4:31 AM, Zalikha Ibrahim
> <zalikha.ibrahim.yahoo.com>wrote:
>
> > Hi Bill,
> >
> > Checked the directory, and it is drwxrwxr-x
> > It successfully read the prmtop, but not the mdcrd.
> >
> > The msg printed is as below:
> >
> > PTRAJ: trajin prod.mdcrd
> > Checking coordinates: prod.mdcrd
> >
> > Could not open file (prod.mdcrd) with mode (r)
> > WARNING in checkCoordinates(): Could not open file (prod.mdcrd)
> > WARNING in ptrajSetupIO(): trajin prod.mdcrd, cannot open file...
> >
> > PTRAJ: rms first mass out prod_rmsd.out .N, CA, C
> > Mask [.N,] represents 663 atoms
> > WARNING in ptraj(): No input trajectories specified (trajin), aborting...
> >
> > is that because the file is too large?
> >
>
> That should have no bearing on it. I'm sure people have read in files much
> larger. What happens if you try to look at the head of that file, what
> happens?
>
> head prod.mdcrd
>
> If it is a NetCDF file, try using ncdump instead:
>
> ncdump prod.mdcrd | head
>
> If permission is still denied, then it's not an Amber error and we're
> limited in our ability to help.
>
> If it works (i.e., you get output), then it may be an Amber error, in which
> case, try using cpptraj instead to see if the error goes away.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Wed Sep 26 2012 - 03:00:02 PDT
