AMBER Archive (2004)

Subject: RE: AMBER: Problem with sander - Error on Open

From: Mike (amber_list_at_speedpost.net)
Date: Thu Jul 08 2004 - 20:57:43 CDT

Hi Ross,

Thanks for your quick reply...I already had that file to be overwritten
( -O option) and my input file name is mdin..

This is my sander script for minimisation

cat <<eof >mdin
  mimimize
 &cntrl
   imin=1, maxcyc=100, rbornstat=1,
   cut=999.0, igb=5, saltcon=0.2,
   ntpr=1, ntx=1, ntb=0, dt=0.001, gbsa=1,
   nstlim = 1000, irest=0,
 &end
eof
sander -O -i mdin \
       -o sample.out -c sample.crd -p sample.top

What is confusing me is that the same (exactly same) script worked 2
days ago and i don't know what happened now..

So, can you please tell me what is wrong?

Any help would be greatly appreciated.

Thanks

Mike

On Thu, 8 Jul 2004 15:15:04 -0700, "Ross Walker" <ross_at_rosswalker.co.uk>
said:
> 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
> -O.
>
> 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
> http://amber.scripps.edu/tutorial/index.html. 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
> 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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