What does
echo $AMBERHOME
return? (and if you can see where I'm going with this, make sure AMBERHOME
is set).
All the best,
Jason
On Sat, Apr 2, 2011 at 12:08 PM, Mahmoud Soliman <mahmoudelkot.gmail.com>wrote:
>
> Hi Amber experts,
> I am trying to run mm_pbsa.pl script to extract coordinates from the
> trajectory but I keep getting this error message below, I do not know
> whether or not it is something due to installation problem on our cluster
> (IT support does not provide too much attention and always responds to
> our
> emails one year later) or due to some problem in my script to run the job
> (see below)
> the command I use is
> /export/home/nmonama/amber/bin/mm_pbsa.pl extract_coords.mmpbsa >
> extract_coords.log
> error is
> Use of uninitialized value in concatenation (.) or string at
> /export/home/nmonama/amber/bin/mm_pbsa.pl line 22.
> Can't locate mm_pbsa_global.pm in .INC (.INC contains: /src/mm_pbsa
> /usr/lib/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8
> /usr/lib/perl5/site_perl/5.8.8/x86_64-linux-thread-multi
> /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl
> /usr/lib/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi
> /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl .) at
> /export/home/nmonama/amber/bin/mm_pbsa.pl line 23.
> BEGIN failed--compilation aborted at
> /export/home/nmonama/amber/bin/mm_pbsa.pl line 23.
> My input script is
> .GENERAL
> PREFIX snapshot
> PATH ./
> COMPLEX 1
> RECEPTOR 1
> LIGAND 1
> COMPT ./com.top
> RECPT ./rec.top
> LIGPT ./lig.top
> GC 1
> AS 0
> DC 0
> MM 0
> GB 0
> PB 0
> MS 0
> NM 0
> .MAKECRD
> BOX YES
> NTOTAL 20647
> NSTART 1
> NSTOP 100
> NFREQ 1
> NUMBER_LIG_GROUPS 1
> LSTART 2772
> LSTOP 2818
> NUMBER_REC_GROUPS 1
> RSTART 1
> RSTOP 2771
> .TRAJECTORY
> TRAJECTORY ./5nsmd.mdcrd
> .PROGRAMS
> any help would be appreciated
> best wishes
> Mahmoud
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sat Apr 02 2011 - 12:30:02 PDT
