Hi to all,
I am currently re-running the simulation, as suggested.
I would like to thank all community members for wise suggestions and help. I learn a lot here
Zalikha
________________________________
From: Bill Ross <ross.cgl.ucsf.EDU>
To: amber.ambermd.org; zalikha.ibrahim.yahoo.com
Sent: Friday, September 28, 2012 6:08 AM
Subject: Re: [AMBER] Could not open mdcrd file with mode (r)
The fact anything appeared shows that it's readable by your acct.
Bill
Zalikha Ibrahim <zalikha.ibrahim.yahoo.com> wrote:
> 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 Sun Sep 30 2012 - 01:30:02 PDT
