Bill,
I have tried to look at the head of the file - unreadable symbols appeared. You can check it in my previous reply.
Thanks so much for your help and suggestion
________________________________
From: Bill Ross <ross.cgl.ucsf.EDU>
To: amber.ambermd.org; zalikha.ibrahim.yahoo.com
Sent: Wednesday, September 26, 2012 7:48 AM
Subject: Re: [AMBER] Could not open mdcrd file with mode (r)
> 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...
It would be great if ptraj printed the error it got from the system.
Can you 'head prod.mdcrd'?
Bill
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?
>
>
>
> ________________________________
> 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 Wed Sep 26 2012 - 02:30:03 PDT
