On Thu, May 19, 2011 at 2:46 PM, Jagur Lambix <jagurlambix.yahoo.com> wrote:
> Hello AMBER users,
>
> I am calculating the binding free energy of a complexed protein-ligand
> system .
>
> However while extracting the snapshots with the command below, it shows the
> following message:
>
> $ set AMBERHOME=/usr/apps/chemistry/amber/amber11
>
If you are using a csh derivative (tcsh, csh, etc.), use "setenv" instead of
set. If you are using bash or some other sh derivative, use "export".
>
> $ $AMBERHOME/exe/mm_pbsa.pl extract_coords.mmpbsa > extract_coords.log
>
> Use of uninitialized value $ENV{"AMBERHOME"} in concatenation (.) or string
> at /usr/apps/chemistry/amber/amber11/exe/mm_pbsa.pl line 22.
> Can't locate mm_pbsa_global.pm in .INC (.INC contains: /src/mm_pbsa
> /usr/lib/perl5/5.10.0/x86_64-linux-thread-multi /usr/lib/perl5/5.10.0
> /usr/lib/perl5/site_perl/5.10.0/x86_64-linux-thread-multi
> /usr/lib/perl5/site_perl/5.10.0
> /usr/lib/perl5/vendor_perl/5.10.0/x86_64-linux-thread-multi
> /usr/lib/perl5/vendor_perl/5.10.0 /usr/lib/perl5/vendor_perl .) at
> /usr/apps/chemistry/amber/amber11/exe/mm_pbsa.pl line 23.
> BEGIN failed--compilation aborted at /usr/apps/chemistry/amber/amber11/exe/
> mm_pbsa.pl line 23.
>
> I didn't understand the message very clearly. Can anyone please let me know
> how to solve this issue. What commands can be used instead to set the
> AMBERHOME ?
>
> Please let me know. Your suggestions in this regard is highly appreciated.
>
> Thanks
> Jagur
>
>
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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 Thu May 19 2011 - 20:30:03 PDT
