AMBER Archive (2008)

Subject: Re: AMBER: Set 251 is corrupted, ptraj error...

From: Waqas Nasir (nasirwaqas1983_at_yahoo.com)
Date: Tue Aug 05 2008 - 06:23:47 CDT

Thanks dac. I should have had figured it out myself, thanks again!

Stay blessed!
Kind regards,
Waqas.

----- Original Message ----
From: David A. Case <case_at_scripps.edu>
To: amber_at_scripps.edu
Sent: Monday, August 4, 2008 5:31:28 PM
Subject: Re: AMBER: Set 251 is corrupted, ptraj error...

On Mon, Aug 04, 2008, Waqas Nasir wrote:
>
> I am using amber version 8...

> PTRAJ: Successfully read the input file.
> | | | | | | Coordinate processing will occur on 250 frames.
>
> INPUT COORDINATE FILES
> | File (input.mdcrd) is an AMBER trajectory with 250 sets
>
>
> Processing AMBER trajectory file input.mdcrd
>
> Set| | | | | 1 .................................................
> Set| | | | 50 .................................................
> Set| | | 100 .................................................
> Set| | | 150 .................................................
> Set| | | 200 .................................................
> Set| | | 250
> ERROR in readAmberTrajectory(): Set #251 is corrupted (
> (??? X5P\H??????N???)...

This is a bogus error message, that doesn't cause any problems. You
have 250 frames in the trajectory (see above mesages), and old versions
of ptraj would often complain that set 251 (which isn't there at all) is
"corrupted".

You might really consider updating to the latest version of ptraj, see
http://ambermd.org/#AmberTools.

...dac

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