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
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
Received on Wed Sep 01 2010 - 17:30:03 PDT
