AMBER Archive (2004)

Subject: Re: AMBER: error message about the input file of sander

From: Ru-Zhen Li (r.li_at_qmul.ac.uk)
Date: Tue Nov 09 2004 - 06:49:26 CST

Dear all,

just want to say that I checked the .out file, and solved the problem by
adding a new line with &end after the "/", one empty column before the &end.
just in case other people might have the same problem in the future.

cheers!
RZ
**********************************************************************
Ms Ru-Zhen Li

0044-020-78826327
r.li_at_qmul.ac.uk
http://www.freewebs.com/lrz/
Materials Department
Queen Mary
University of London
E1 4NS
**********************************************************************
----- Original Message -----
From: "Michael Crowley" <crowley_at_scripps.edu>
To: "Ru-Zhen Li" <r.li_at_qmul.ac.uk>
Cc: <amber_at_scripps.edu>
Sent: Tuesday, November 09, 2004 6:48 AM
Subject: Re: AMBER: error message about the input file of sander

> Ru-Zhen,
>
> your namelist needs to end with a
> /
>
> make sure that there is a new line after the terminating "/"
> some editors will leave out the last newline if you do not put it in
> explicitly.
>
> Mike
>
> -----------------------------------------------------------------
> Physical mail: Dr. Michael F. Crowley
> Department of Molecular Biology, TPC6
> The Scripps Research Institute
> 10550 North Torrey Pines Road
> La Jolla, California 92037
>
> Electronic mail: crowley_at_scripps.edu
> Telephone: 858/784-9290
> Fax: 858/784-8688
> -----------------------------------------------------------------
>
> On Tue, 9 Nov 2004, Ru-Zhen Li wrote:
>
>> Dear all,
>>
>> I got an error message when I tried to use sander,
>>
>> $AMBERHOME/exe/sander -O -i 1iyt_vac_init_min.in -o
>> 1iyt_vac_init_min.out -c
>> 1iyt_vac.inpcrd -p 1iyt_vac.prmtop -r 1iyt_vac_init_min.rst
>>
>> then it said:
>>
>> namelist read: no end record
>> apparent state: unit 5 named 1iyt_vac_init_min.in
>> last format: namelist io
>> Unit 5 is a sequenctial formatted external file
>> ***Execution Terminated (120)***
>>
>> I am new user, I followed the instruction from the tutorial, and then I
>> used
>> the files from the tutorial, the same error message came out. I noticed
>> that
>> nobody has mentioned this error before.
>>
>> this is the input file
>>
>> polyA-polyT 10-mer: initial minimisation prior to MD
>> &cntrl
>> imin = 1,
>> maxcyc = 500,
>> ncyc = 250,
>> ntb = 0,
>> igb = 0,
>> cut = 12 (I tried both with "," and without it here, and it is the
>> same
>> error)
>> /does anyone have any idea about this?Thanks!RZ
>> **********************************************************************Ms
>> Ru-Zhen Li
>> 0044-020-78826327
>> r.li_at_qmul.ac.uk
>> Materials Department
>> Queen Mary
>> University of London
>> E1 4NS
>> **********************************************************************
>>
>> -----------------------------------------------------------------------
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>
>

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