Dear Jason,
Thanks. I really appreciate your suggestions.
Tried to look at the head of that file (head prod.mdcrd), it printed out unreadable symbols
Also tried to use cpptraj, it printed out this message:
INPUT: Reading Input from file prod_rmsd.ptraj
[trajin prod_1wd9_solvbox8.mdcrd]
Warning: prod_1wd9_solvbox8.mdcrd: UNKNOWN FILE FORMAT.
ERROR: Setting up file for trajectory prod_1wd9_solvbox8.mdcrd
[rms first mass out prod_rmsd.out .N, CA, C]
TRAJECTORIES:
Coordinate processing will occur on 0 frames.
PARAMETER FILES:
0: 1wd9_solvbox8.prmtop, 112372 atoms, 34667 res, boxtype 1, 34005 mol, 33984 solvent mol, 0 frames.
REFERENCE COORDS:
No reference coordinates.
No frames defined.
OUTPUT TRAJECTORIES:
No files.
probably due to wrong input?
________________________________
From: Jason Swails <jason.swails.gmail.com>
To: Zalikha Ibrahim <zalikha.ibrahim.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Tuesday, September 25, 2012 7:24 PM
Subject: Re: [AMBER] Could not open mdcrd file with mode (r)
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 - 02:30:02 PDT
