AMBER Archive (2002)

Subject: Re:

From: Carlos Simmerling (carlos.simmerling_at_sunysb.edu)
Date: Sat Apr 13 2002 - 07:06:29 CDT

check for NMRMAX or NTCM. both
are no longer supported but show up at various
spots in that tutorial. just remove them- the
default settings for the related variables are
usually ok. check the manual for details.
Carlos Simmerling

----- Original Message -----
From: "Mark Hsieh" <hsieh_at_abmaxis.com>
To: <amber_at_heimdal.compchem.ucsf.edu>
Sent: Wednesday, April 10, 2002 4:31 PM

> I'm trying to run the tutorials for amber7 but cannot get the
> dynamics to run for the DNA example with explicit solvents:
>
> http://www.amber.ucsf.edu/amber/tutorial/polyA-polyT/equilibration.html
>
> Specifically, I run
>
> sander -O -i min_ntr.in \
> -o min_ntr.out \
> -c parm.inpcrd \
> -p parm.prmtop \
> -r min_ntr.restrt \
> -ref parm.inpcrd
>
> with "polyAT.inpcrd" and "polyAT.prmtop" from earlier steps substituted
> in for "parm.inpcrd" and "parm.prmtop".
>
> I get the error message:
>
> namelist read: variable not in namelist
> apparent state: unit 5 named md_ntr.in
> last format: list io
> lately reading sequential formatted external IO
> Aborted
>
> Is there a mismatch between the namelist and the variables in md_ntr.in?
>
> How can I fix this so that I can continue with the tutorial?
>
> Thank you,
> Mark Hsieh
>