AMBER Archive (2004)

Subject: Re: AMBER: trajectory file corruption

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Tue Jan 27 2004 - 12:54:30 CST

> On Tue, 2004-01-27 at 03:11, John wrote:
> > Hello All,
> >
> > I successfully completed a 500ps production MD. The pdb file I created using
> > the rst file looks reasonable in VMD. When I tried to use the trajectory
> > file VMD could not read the file. After opening it I realised that it has
> > been totally corrupted and has nothing to do with a normal molecular
> > dynamics trajectory file.
>
> Check your input file, it looks like you requested a binary
> trajectory file. You can probably still salvage it via ptraj/carnal.

If the file was written as binary (is this possible for mdcrd?),
you may need to write a small fortran program to convert it to
formatted. Carnal doesn't read binary files. The format of binary
files can differ from one machine to another, so it is safest
to compile/run the conversion program on the machine that wrote
the file.

Another possibility is that the file was corrupted. This might be
more likely if it was written to a remotely-mounted filesystem and
the file was really big (as often happens with mdcrd's). Details
of your environment would be useful here.

Bill Ross

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