AMBER Archive (2009)

Subject: Re: [AMBER] normal mode analysis

From: David A. Case (
Date: Mon May 04 2009 - 13:06:32 CDT

On Mon, May 04, 2009, Hannes Wallnoefer wrote:
> It seems as if you are right. I changed the default of the
> script for ntxo from 0 to 1, because the default is not allowed in
> amber10 any more. If i use amber9 with ntxo = 0 minimization the nmode
> tool works fine. Is there an alternative to using amber9 for the normal
> mode analysis?

It should be necessary just to make sander and nmode the same (i.e. both
formatted). But I don't use these particular scripts, so maybe people on the
list can chime in with ideas here.


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