AMBER Archive (2002)

Subject: Re: a missing variable

From: Matthew Randolph Lee, Ph.D. (mrlee_at_sd.lionbioscience.com)
Date: Wed Aug 28 2002 - 17:27:12 CDT

It looks like you need the following lines at the bottom of your input
file, which are to deal with a section FOUR (see page 85 of amber7
manual). Whenever you set nmropt=1, you have to deal with section TWO &
FOUR.
--------------
 &rst
 &end
--------------

Alternatively, you could "touch" an empty DISANG file and specify it in a
section THREE (see page 85) with
--------------
DISANG=filename
--------------

--Matt

On Wed, 28 Aug 2002, Vlad Cojocaru wrote:

> Hi! I have a problem. I am using the following script:
>
> # MD with heating to 1000K and then cooling down back to 300K
> &cntrl
>
> nmropt = 1,
> ntx = 1, irest = 0, ntrx = 1, ntxo = 1,
> ntpr = 50, ntwx = 100, ntwv = 0, ntwe = 0,
>
> ntf = 2, ntb = 2,
> cut = 9.0, nsnb = 10,
>
> ibelly = 0, ntr = 1,
>
> imin = 0,
> nstlim = 15000,
> nscm = 0,
> t = 0.0, dt = 0.001,
>
> tempi = 300.0,
> ig = 71277, heat = 0.0,
> ntt = 1,
>
> ntp = 1, pres0 = 1.0,
>
> ntc = 2, tol = 0.00001,
> vlimit=15,
>
> &end
>
> &wt
> type='TEMP0', istep1=0, istep2=1000,
> value1=300.0, value2=1000.0,
> &end
> &wt
> type='TEMP0', istep1=1001, istep2=3000,
> value1=1000.0, value2=1000.0,
> &end
> &wt
> type='TEMP0', istep=3001, istep2=15000,
> value1=1000.0, value2=300.0,
> &end
>
> &wt
> type='TAUTP', istep=0, istep2=3000,
> value1=0.2, value2=0.2,
> &end
>
> &wt
> type='TAUTP', istep=3001, istep2=11000,
> value1=2.0, value2=2.0,
> &end
>
> &wt
> type='TAUTP', istep=11001, istep2=13000,
> value1=1.0, value2=1.0,
> &end
>
> &wt
> type='TAUTP', istep=13001, istep2=14000,
> value1=0.5, value2=0.5,
> &end
>
> &wt
> type='TAUTP', istep=14001, istep2=15000,
> value1=0.05, value2=0.05,
> &end
> END
>
> EOF
>
> I get the following error message.
>
> /usr/local/amber7/exe/sander -O -i sander_350.in -p rna_ion_wat.top -c
> rna_ion_wat_mdeq0.rst -ref rna_ion_wat_mdeq0.rst -x
> rna_ion_wat_350.mdcrd -v rna_ion_wat_350.mdvel -e rna_ion_wat_350.mden
> -o rna_ion_wat_350.so -r rna_ion_wat_350.rst -inf rna_ion_wat_350.info
> namelist read: variable not in namelist
> apparent state: unit 5 named sander_350.in
> last format: list io
> lately reading sequential formatted external IO
> Abort
>
> I guess that there is a variable not specified in one of the namelists.
> I could not figger it out yet. Could somebody tell me which one is
> missing?
>
>
>
>
>

*******************************************************************
Matthew Randolph Lee, Ph.D.

Computational Scientist phone: (858)410-6534
Lion Bioscience Inc. fax: (858)410-6665
9880 Campus Point Drive e-mail: matthew.lee_at_lionbioscience.com
San Diego, CA 92121
*******************************************************************