AMBER Archive (2004)

Subject: Re: AMBER: problem in quasih.f diagonalising matrix

From: David A. Case (
Date: Mon Nov 29 2004 - 10:38:46 CST

On Mon, Nov 29, 2004, Phineus Markwick wrote:
> I am having difficulties with the quasiharmonic analysis routine in AMBER 7.
> The program reads in all the coordinates and mass file, generates an
> average structure
> which it writes to file xyz and constructs the matrix A. However, even
> after running for 2 days
> no further output (nor error message) is written.

I don't see anything in your description that could cause this. You could
try a test of stripping even more of your molecule away (to get a very
small system) and see if that would complete.

(I'm assuming you have run the quasih test case in the Amber 7 distribution,
and that that is OK.)

The "interactive essential dynamics" package (see the link on the Amber web
page) might also help; or, you could update to Amber 8 and see if the analysis
routines there (which are now a part of ptraj itself) would work.

...good luck....dac

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to