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 - 14:33:57 CST

Hi Ross,

here is the one that works, and the one which does not work is exactly the
same except the line with "&end"

I am running it on A SGI Origin 300 system with 16 MIPS R14000 processors
and 16 GBytes memory, which is in CSAR, one of the High Performance Centres
in UK, the shell is ksh, and editor I used is vi. because I am a new user of
this machine, i do not know too much about it. if there is anything you want
to know, I will try to get the answer from the support team.

cheers!

Best regards,
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: "Ross Walker" <ross_at_rosswalker.co.uk>
To: <amber_at_scripps.edu>
Sent: Tuesday, November 09, 2004 5:44 PM
Subject: RE: AMBER: error message about the input file of sander

> Hi Ru,
>
>> 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.
>
> This is strange. All the test cases and tutorials used to have the format
>
> Title
> &cntrl
> var1=1,var2=2,
> var3=3,
> &end
>
> But some compilers didn't like the &end which is not the official standard
> for namelists. The official standard is to use a / as in:
>
> Title
> &cntrl
> var1=1,var2=2,
> var3=3,
> /
>
> With no &end. So it is strange to find on your system that the reverse is
> true. Can you possibly send me the two input files you used, the one that
> didn't work an the one that did. Can you also let me know what your system
> is and what compilers / versions you are using.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | Department of Molecular Biology TPC15 |
> | The Scripps Research Institute |
> | Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk/ | PGP Key available on request |
>
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