AMBER Archive (2002)

Subject: Re: Error decoding variable

From: Rukman Hertadi (rhertadi_at_bio.titech.ac.jp)
Date: Wed Jul 31 2002 - 20:50:27 CDT

Sorry, this was my mistake to send the real input file, Actually the input
file as follow

Warm the system up
&cntrl
imin,
ntxst
ntxo0, ntwr0,
ntfielcut€, scee,
nstlim%000, nscm0, dt
nttutp ,
ntc,
&end
#
&wt typevalue2P.0, &end
&wt typevalue20.0, &end
&wt typevalue2 0.0, &end
&wt typevalue2%0.0, &end
&wt typevalue200.0, &end
&wt typevalue200.0, &end
&wt type#
Group for restrained atom
10.0
RES 1 29
END
END

Could you please explain why the problem was occured. Does in this case I
have to prepare the restrain file seperately as written in the manual. Why
ntroes not compatible with nmropt option. My system contains about 25000
atoms, this number of atom can not be handled by makeDIST_RST or other
restrain programs available in AMBER that has a limit capability of 5000
atom.
-------Original Message-------

From: Carlos Simmerling
Date: 2002”N8ŒŽ1“ú 1:02:28
To: jim caldwell; Rukman Hertadi
Cc: AMBER Group
Subject: Re: Error decoding variable

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,
> > ntxst
> > ntxo0, ntwr0,
> > ntr
> > ntfielcut€, scee,
> > nstlim 000, nscm0, dt
> > nttutp ,
> > tempiP, temp000,
> > ntc
> > &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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