AMBER Archive (2004)

Subject: Re: AMBER: LINMIN failure

From: Robyn Ayscue (
Date: Thu Jun 10 2004 - 06:52:07 CDT

Hi! I looked at your .in file, and it looks like you
don't have anything set for the NCYC variable, so
Sander sets the default at NCYC=10, meaning that after
10 cycles conjugate gradient minimization will be
turned on. When you have a solvated system then the
conjugate gradient method can overwhelm Sander and
it'll often give you that LINMIN error. To avoid it,
try including a tag in your .in file of NCYC=500. As
long as you keep NCYC greater than MAXCYC, the
conjugate gradient is never turned on.

Robyn Ayscue

--- Mizuguchi Mineyuki <>
> Hello, Amber
> I am energy-minimizing the system containing a
> protein and TIP3 water
> moleclues.
> But something is wrong, and the output file says
> Attached files are input and output files. Could
> someone advise and help
> me?
> Sincerely,
> Mineyuki

> ATTACHMENT part 2 application/octet-stream

> ATTACHMENT part 3 application/octet-stream

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