On Mon, Sep 5, 2011 at 1:49 PM, Rajesh Raju
<rajesh.raju.mail.chem.tamu.edu>wrote:
> Dear AMBER USERS,
>
> I used NAB module implemented in the ambertools 1.5 for making a
> 10-mer structure of a BDNA complex. I used the same input given in
> the section 13.5.1 (Page 240 AMBER tools manual).
>
>
> // Program 1 - Average B-form DNA duplex
> molecule m;
>
> m = bdna( "gcgttaacgc" );
> putpdb( "gcg10.pdb", m );
>
>
> When I complied with the command nab nuc.nab it was giving an error
> message of
>
> /g/software/lms/ambertemp/amber11/bin/ucpp: No such file or directory
> cpp failed!
>
It looks like Amber11 was installed in a temporary directory and then moved
into a new position. The problem with doing this is that AMBERHOME is
hard-coded into nab at compile-time, so when AMBERHOME is changed, you get
errors like these.
Strangely enough, in many cases this issue can actually be solved with sed,
of all things. If you have access to the nab program, run the following
command:
sed -i -e "s./g/software/lms/ambertemp/amber11/bin.$AMBERHOME/bin.g"
$AMBERHOME/bin/nab
If you don't have permission to modify that file, ask whoever does have
permission to do that.
To avoid this issue in the future (for either you or whoever built this in
the first place), be aware that amber is not meant to be moved after it's
been compiled (quite nontraditional, so it's not surprising that computer
admins would try this, although it would make every nab test fail after it
was done).
HTH,
Jason
> This is the first time Iam using NAB. Can anyone pls help me..
>
> Thanks
> Rajesh
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Sep 05 2011 - 16:00:06 PDT
