Hello,
On Wed, Sep 1, 2010 at 8:18 PM, Siddharth Rastogi <
siddharthrastogi08.gmail.com> wrote:
> Hello Dwight & Jason,
>
> Thank you for your valuable suggestions.
> Yeah, I have applied all the bug fixes for AMBER 10 version.
>
> Also I set the AMBERHOME in addition to the bug fixes, but the same problem
> persists.
>
> The command I followed are as follows:
>
> $ set AMBERHOME=/usr/apps/amber10/
> $ export AMBERHOME
> $ $AMBERHOME/exe/mm_pbsa.pl extract_coords.mmpbsa > extract_coords.log
> -bash: /exe/mm_pbsa.pl: No such file or directory
>
This right here tells you that $AMBERHOME returns nothing, since it's
complaining that "/exe/mm_pbsa.pl" can't be found. Do not use the "set"
statement above. Try the following:
export AMBERHOME=/usr/apps/amber10
$AMBERHOME/exe/mm_pbsa.pl extract_coords.mmpbsa > extract_coords.log
If you want to check that AMBERHOME has actually been set, use the following
command:
/usr/bin/env | grep AMBERHOME
Good luck!
Jason
>
> Again I did like as before, but the same. I couldn't go elsewhere.
>
> $ /usr/apps/amber10/exe/mm_pbsa.pl extract_coords.mmpbsa >
> extract_coords.log
>
> Use of uninitialized value in concatenation (.) or string at
> /usr/apps/amber10/exe/mm_pbsa.pl line 22.
> Can't locate mm_pbsa_global.pm in .INC (.INC contains: /src/mm_pbsa
> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi
> /usr/lib64/perl5/site_perl/5.8.7/x86_64-linux-thread-multi
> /usr/lib64/perl5/site_perl/5.8.6/x86_64-linux-thread-multi
> /usr/lib64/perl5/site_perl/5.8.5/x86_64-linux-thread-multi
> /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl/5.8.7
> /usr/lib/perl5/site_perl/5.8.6 /usr/lib/perl5/site_perl/5.8.5
> /usr/lib/perl5/site_perl
> /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi
> /usr/lib64/perl5/vendor_perl/5.8.7/x86_64-linux-thread-multi
> /usr/lib64/perl5/vendor_perl/5.8.6/x86_64-linux-thread-multi
> /usr/lib64/perl5/vendor_perl/5.8.5/x86_64-linux-thread-multi
> /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl/5.8.7
> /usr/lib/perl5/vendor_perl/5.8.6 /usr/lib/perl5/vendor_perl/5.8.5
> /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi
> /usr/lib/perl5/5.8.8 .) at /usr/apps/amber10/exe/mm_pbsa.pl line 23.
> BEGIN failed--compilation aborted at /usr/apps/amber10/exe/mm_pbsa.pl line
> 23.
>
> Any more suggestions is always appreciated.
>
> Thanks
> Siddharth
>
>
> On Wed, Sep 1, 2010 at 9:31 AM, Dwight McGee <dwight.mcgee.gmail.com>
> wrote:
>
> > Hi,
> >
> > Have you applied all the bug fixes?
> >
> > On Wed, Sep 1, 2010 at 11:10 AM, Siddharth Rastogi <
> > siddharthrastogi08.gmail.com> wrote:
> >
> > > Dear AMBER users,
> > >
> > > I am doing some MM-PBSA Calculation for my protein-ligand complex.
> > > However, I was just following the tutorial in the AMBER web page by
> Ross
> > > Walker.
> > > In the mean time I got the error as follows:
> > >
> > > Use of uninitialized value in concatenation (.) or string at
> > > /usr/apps/amber10/exe/mm_pbsa.pl line 22.
> > > Can't locate mm_pbsa_global.pm in .INC (.INC contains: /src/mm_pbsa
> > > /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi
> > > /usr/lib64/perl5/site_perl/5.8.7/x86_64-linux-thread-multi
> > > /usr/lib64/perl5/site_perl/5.8.6/x86_64-linux-thread-multi
> > > /usr/lib64/perl5/site_perl/5.8.5/x86_64-linux-thread-multi
> > > /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl/5.8.7
> > > /usr/lib/perl5/site_perl/5.8.6 /usr/lib/perl5/site_perl/5.8.5
> > > /usr/lib/perl5/site_perl
> > > /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi
> > > /usr/lib64/perl5/vendor_perl/5.8.7/x86_64-linux-thread-multi
> > > /usr/lib64/perl5/vendor_perl/5.8.6/x86_64-linux-thread-multi
> > > /usr/lib64/perl5/vendor_perl/5.8.5/x86_64-linux-thread-multi
> > > /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl/5.8.7
> > > /usr/lib/perl5/vendor_perl/5.8.6 /usr/lib/perl5/vendor_perl/5.8.5
> > > /usr/lib/perl5/vendor_perl
> > /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi
> > > /usr/lib/perl5/5.8.8 .) at /usr/apps/amber10/exe/mm_pbsa.pl line 23.
> > > BEGIN failed--compilation aborted at
> /usr/apps/amber10/exe/mm_pbsa.plline
> > > 23.
> > >
> > >
> > >
> > > I didn't understand the full error message.
> > > So I tried to find it out from the AMBER mailing list.
> > > I got one same type of posting (
> > > http://archive.ambermd.org/200809/0335.html),
> > > but unfortunately no reply to this question.
> > >
> > > I have also this problem with both amber 9 and 10.
> > > Is it a problem with the installation ?
> > > So can any one suggest, what is going on here.
> > > Thank you for your suggestions.
> > >
> > >
> > > Thanks
> > >
> > > --
> > > Siddharth Rastogi
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > T. Dwight McGee Jr.
> > Quantum Theory Project
> > University of Florida
> > Graduate Student
> > dwight.mcgee.gmail.com
> >
> > "Problems cannot be solved at the same level of awareness that created
> > them."
> > Albert Einstein
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Siddharth Rastogi
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Sep 01 2010 - 19:00:04 PDT
