AMBER Archive (2008)

Subject: Re: AMBER: problem with nmod

From: David A. Case (
Date: Fri Mar 28 2008 - 19:19:40 CDT

On Fri, Mar 28, 2008, yuri pomè wrote:

> During ligand only sander minimization I get an
> error due to "LINMIN FAILURE", it sounds strange for a system with
> only 34 atoms.

Not necessarily strange, or unexpected, especially given the behavior you
report below.

> During minimization the conjugated gradient works bad so the ligand
> reach a linmin failure (drms reach 0.1 at most), with steepest-descent
> (manually editing ncyc=100000, maxcyc=200000, drms=0,0001) I
> can reach a drms of 0,0004 (for example), but when conjugate grad
> starts I got this error:
> "The system has extended beyond
> the extent of the virtual box.

Something bad is happening to the coordinates during the minimization. Since
there are only 34 atoms, you should be able to visualize or manually examine
the coordinates to get an idea of what the problem is. My guess is that if
you follow the coordinates during the course of the minimization, you will
get some clues that will help.

...good luck...dac

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