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?
________________________________
From: Bill Ross <ross.cgl.ucsf.EDU>
To: amber.ambermd.org
Sent: Tuesday, September 25, 2012 11:13 AM
Subject: Re: [AMBER] Could not open mdcrd file with mode (r)
> > 1) I have a mdcrd file with the size almost 4 GB. I tried to proceed
> > checking rmsd using ptraj, but it gave me warning 'could not open mdcrd
> > file with mode (r)'. I searched in archive, and found that the problem
> > might due to file permission. So I change the mode from rw-rw-r to
> > rwxrwx--x, but still it didnt work. I would be grateful if anyone could
> > help me how to solve this, so that I can proceed with analysis.
The x's should have no effect on read access for files, but do
matter for directories.
Check the ownership and permissions of the containing directory, too.
Is no further error msg printed? I would expect one.
Bill
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Received on Tue Sep 25 2012 - 02:00:03 PDT
