AMBER Archive (2002)

Subject: Re: Error decoding variable

From: Carlos Simmerling (carlos.simmerling_at_sunysb.edu)
Date: Wed Jul 31 2002 - 10:41:04 CDT

I agree with Jim but suspect you haven't given us the whole input file
since the SANDER output "Warm the system up" doesn't appear in the
quoted input file. Maybe the title was omitted too?

We need to see your entire input file to be able to help you.
Carlos

> > ----- READING GROUP 1; TITLE:
> > Warm the system up

----- Original Message -----
From: "jim caldwell" <caldwell_at_heimdal.compchem.ucsf.edu>
To: "Rukman Hertadi" <rhertadi_at_bio.titech.ac.jp>
Cc: "AMBER Group" <amber_at_heimdal.compchem.ucsf.edu>
Sent: Wednesday, July 31, 2002 10:43 AM
Subject: Re: Error decoding variable

>
> The input file must look like:
>
> title line
> &cntrl
> variables
> &end
> .
> .
>
>
> Note the "&cntrl" must start in column 2 of line 2.
>
>
> On Wed, 31 Jul 2002, Rukman Hertadi wrote:
>
> > Dear Amber users
> >
> > I just tried to equilibrate a system using sander (AMBER 7). The input
file
> > as follow:
> > &cntrl
> > imin=0, nmropt=1,
> > ntx=1, irest=0,
> > ntxo=1, ntpr=10, ntwr=100,
> > ntr=1,
> > ntf=1, ntb=1, dielc=1, cut=8.0, scee=1.2,
> > nstlim=20000, nscm=100, dt=0.001,
> > ntt=1, tautp=2.0,
> > tempi=50, temp0=300,
> > ntc=1,
> > &end
> > Group of input atoms
> > 10.0
> > RES 1 24
> > END
> > END
> >
> > But the calculation produced the following error message:
> > LOADING THE CONSTRAINED ATOMS AS GROUPS
> >
> >
> > 5. REFERENCE ATOM COORDINATES
> >
> >
> >
> > ----- READING GROUP 1; TITLE:
> > Warm the system up
> >
> > rfree: Error decoding variable 1 3 from:
> > &cntrl
> >
> > Can anybody help me to figure out what the meaning of this error? How to
fix
> > it?
> >
> > Thank in advance.
> >
> > Rukman Hertadi
> >
> > Laboratory of Biodynamics
> > Graduate School of Bioscience and Biotechnology
> > Tokyo Institute of Technology
> > 4259 Nagatsuta-cho, Midori-ku, Yokohama,
> > Kanagawa 226-8501, Japan.
> > Phone: +81-45-924-5739
> > FAX: +81-45-924-5806
> > email: rhertadi_at_bio.titech.ac.jp
> >
> >
>
>
> -------------------------------------------------------------------------- 

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