AMBER Archive (2009)

Subject: RE: [AMBER] error in constructing DNA from nucgen

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Mar 17 2009 - 14:31:16 CDT

Does the nuc.out file already exist? If so then nucgen will not overwrite
it. You need to remove the output files first.

Ross

> -----Original Message-----
> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> Behalf Of Pansy Patel
> Sent: Tuesday, March 17, 2009 12:25 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] error in constructing DNA from nucgen
>
> Ye s I do have write permissions
> ans I tested it on the example file from the tutorials also
> which worked without errors
>
> Pansy
>
> >>> Carlos Simmerling <carlos.simmerling_at_gmail.com> 3/17/2009 2:53 PM >>>
> are you in a directory where you have write permissions?
> try to create a test file and see if you can. do ls -la and make sure
> things are writable and owned by you.
> if you're not sure how to interpret unix permissions, there is a nice
> unix tutorial at
> http://www.ee.surrey.ac.uk/Teaching/Unix/
>
>
>
> On Tue, Mar 17, 2009 at 2:43 PM, Pansy Patel <pdpatel_at_mail.ucf.edu> wrote:
> > Hello
> >
> > I am trying to construct an AB DNA hexamer using nucgen:
> >
> > nucgen -i nuc.in -o nuc.out -d $AMBERHOME/dat/leap/parm/nucgen.dat -p
> nuc.pdb
> > but I get the following error:
> > Unit 6 Error on OPEN: nuc.out
> > Can somebody please tell me what it means and how I can get it to work ?
> >
> > Pansy
> >
> >
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> >
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