Dan,
Your question reminds me about one input I don't understand, the ioutfm=1. -.-
I actually followed a tutorial, it put the ioutfm=1. It was my fault not inspecting the input before running the simulation. I named the output as .mdcrd., and not .nc (does it affect?)
When i try to look at the head using ncdump -h prod.mdcrd, it printed out 'ncdump: prod.mdcrd: NetCDF: Unknown file format'.
Any suggestion?
Zalikha
________________________________
From: Daniel Roe <daniel.r.roe.gmail.com>
To: Zalikha Ibrahim <zalikha.ibrahim.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Wednesday, September 26, 2012 10:36 PM
Subject: Re: [AMBER] Could not open mdcrd file with mode (r)
Hi,
On Wed, Sep 26, 2012 at 3:19 AM, Zalikha Ibrahim
<zalikha.ibrahim.yahoo.com> wrote:
> 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.
This isn't a good sign. The file recognition in ptraj/cpptraj is
fairly robust, so the fact that it fails combined with the unreadable
symbols makes it sound like A) the file is corrupted or B) it is in a
format that is unsupported. Was the file supposed to be an ASCII
trajectory (ioutfm=0) or NetCDF (ioutfm=1)?
-Dan
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Wed Sep 26 2012 - 20:00:03 PDT
