Re: AMBER: Reply regarding PCA with ptraj and IED

From: Hannes Loeffler <>
Date: Wed, 20 Jun 2007 11:43:21 +0900

On Tue, 19 Jun 2007 17:00:37 -0400
"Steve Spronk" <> wrote:

> The magic number for my system was 3333. When I specified only atoms
> .1-3333 in the masks, the calculation ran fine, but specifying a mask of
> .1-3334 led to the warning message.

Well, I guess the magic here is 3333x3=9999 whereas 3334x3=10002. The code
writes the size of the variance-covariance matrix into the
file with only 4 digits. When reading the file, the code reads again only 4
digits which in your case simply fails.

The bug seems to be fixed with bugfix #20 (amber9) but analyze.c, line 668
still writes 4 digits only (I'm not sure what C programs are supposed to do if
the number of digits is larger than the format; just write all digits?).

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Received on Wed Jun 20 2007 - 06:07:43 PDT
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