RE: AMBER: Problem with sander - Error on Open

From: Ross Walker <>
Date: Thu, 8 Jul 2004 15:15:04 -0700

Hi Mike,

> I am new to amber and i am using AMBER 8.0.
> I gotta run MD simulation and when i type sander in the prompt , i am
> getting the following as errors
> " Unit 5 Error on OPEN: mdin "
> or
> " Unit 6 Error on OPEN: mdout"

This could be due to a couple of things. 1) you don't have an input file or
your input file is not called mdin. If your input file is not called mdin
then you should run sander with:

sander -i input_file

With regards to the output file sander by default will NOT overwrite any
existing files so if a file named mdout already exists in the directory you
will get the error above. Either manually delete / move the existing mdout
file. Specify an alternative name for the output file with sander -o
output_filename and/or tell sander to overwrite file with the -O flag sander

Note, if you want to have faith in your results and trust what you are doing
you should really read up on the theory behind molecular dynamics. I also
highly recommend going through the amber tutorials on Amber is not designed to be
used as a "BlackBox".

For a simple introduction start with the DNA tutorial.

I hope this helps.
All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

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Received on Thu Jul 08 2004 - 23:53:00 PDT
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