AMBER Archive (2004)

Subject: RE: AMBER: problems with mdcrd

From: Ross Walker (
Date: Thu Jul 08 2004 - 12:32:04 CDT

Dear Carsten

> PTRAJ: trajin
> Checking coordinates:
> Could not open file ( with mode (r)
> WARNING in checkCoordinates(): Could not open file (
> WARNING in ptrajSetupIO(): trajin, cannot open file...

This error is triggered by the following piece of code in ptraj.c

if ( openFile(&fp, filename, "r") == 0 ) {
            "WARNING in checkCoordinates(): Could not open file (%s)\n",
    return NULL;

>From this code it should be obvious that all this is trying to do is open
the file. It has not actually done any IO on the file at this point. This
means that the problem is with the file being accessed and NOT with its
contents. Are you certain you have the filename correct (including case?) Do
you have read permission to the file? Can you open it in something else like

Also are you sure no other process currently has a lock on this file? You
could try copying the file to a new file and then using this new file:


If the file is on a network drive try copying it to a local drive. Also,
what is the size of this file? Is it bigger than 2GB? If it is this will
cause you problems on a 32bit machine.

Then try using instead.

If this still doesn't work then I would check you log files to see if there
are any reports of read errors etc.

All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

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