Thanks Jason.
I tried with the commands you suggested and it is working now.
Thank you once again.
Siddharth
On Wed, Sep 1, 2010 at 9:30 PM, Jason Swails <jason.swails.gmail.com> wrote:
> 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.plline
> > 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
> _______________________________________________
> 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
Received on Thu Sep 02 2010 - 12:00:03 PDT
