AMBER Archive (2007)

Subject: Re: AMBER: Reply regarding PCA with ptraj and IED

From: Hannes Loeffler (hal_at_iam.u-tokyo.ac.jp)
Date: Tue Jun 19 2007 - 21:43:21 CDT

On Tue, 19 Jun 2007 17:00:37 -0400
"Steve Spronk" <spronk_at_umich.edu> 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
eigenvalue/eigenvector
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?).

Hannes.
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