On Fri, Oct 29, 2010 at 2:13 PM, bin wang <wang_p_z.yahoo.com.cn> wrote:
> Thank you for your suggestion. I removed the last .PROGRAMS and the error
> message changed to:
> Use of uninitialized value in concatenation (.) or string at
> /usr/local/amber10/src/mm_pbsa/mm_pbsa_readinput.pm line 76, <IN> line 58.
> Use of uninitialized value in exists at
> /usr/local/amber10/src/mm_pbsa/mm_pbsa_readinput.pm line 131, <IN> line
> 58.
> Use of uninitialized value in hash element at
> /usr/local/amber10/src/mm_pbsa/mm_pbsa_readinput.pm line 135, <IN> line
> 58.
> /usr/local/amber10/exe/sander -O -i pbsa_com.in -o pbsa_com.1.out
> -c
> ./snapshot_com.crd.1 -p ./com_vac.prmtop not successful
>
> What should I do to test the mmpbsa_pl?
> A production phase is still running, can I apply the bug fixes and
> recompile
> AMBER 10 now?
>
You should probably wait, no way of being sure what's going to happen. The
tests are in $AMBERHOME/src/mm_pbsa/Examples . Take a look at the files in
there. There should also be a Makefile or some other script that you can
use to run the tests. If they pass, try adapting some of those input files.
Good luck!
Jason
>
>
>
>
>
>
> ________________________________
> From: Jason Swails <jason.swails.gmail.com>
> To: AMBER Mailing List <amber.ambermd.org>
> Sent: Fri, October 29, 2010 11:50:13 AM
> Subject: Re: [AMBER] Error message from binding_energy.mmpbsa
>
> Hello,
>
> My comments are below:
>
> On Fri, Oct 29, 2010 at 10:46 AM, bin wang <wang_p_z.yahoo.com.cn> wrote:
>
> > I use this command:
> >
> > $AMBERHOME/exe/mm_pbsa.pl binding_energy.mmpbsa > binding_energy.log
> >
>
> Is there anything below this point in your input file? I'm simply
> speculating here, but try taking .PROGRAMS out of your input file, since
> the
> input parser may be looking for something in this section...
>
> I do have 2 more suggestions: 1st -- if you have not yet applied the bug
> fixes for amber10, I suggest you do so and recompile. 2nd -- Do the
> mm_pbsa.pl tests work? If they do work, start with one of the input files
> from the test cases and modify it until you get it to what you want. You
> should be able to determine what exactly is breaking with your simulation,
> or better yet, it may just work if your mistake is a trivial one that's
> difficult to find.
>
> Good luck!
> Jason
>
>
> >
> >
> > In mm_pbsa_readinput.pm, the line 76 is:
> > print " Found $key => $value\n";
> > Line 260 is:
> > $r_pro->{$key} = $value; # Overwriting of entries allowed here
> since
> > # default is set in &init_data()
> >
> >
> >
> >
> >
> > ________________________________
> > From: Bill Miller III <brmilleriii.gmail.com>
> > To: AMBER Mailing List <amber.ambermd.org>
> > Sent: Fri, October 29, 2010 11:09:03 AM
> > Subject: Re: [AMBER] Error message from binding_energy.mmpbsa
> >
> > Can you show your input? And what is on lines 76 and 260 of
> > mm_pbsa_readinput.pm?
> >
> > -Bill
> >
> > On Fri, Oct 29, 2010 at 10:50 AM, bin wang <wang_p_z.yahoo.com.cn>
> wrote:
> >
> > > Hello,
> > > I use the binding_energy.mmpbsa from the tutorial A3 to calculate
> binding
> > > energy. But I got these error messages:
> > > Use of uninitialized value in concatenation (.) or string at
> > > /usr/local/amber10/src/mm_pbsa/mm_pbsa_readinput.pm line 76, <IN> line
> > 59.
> > > Use of uninitialized value in hash element at
> > > /usr/local/amber10/src/mm_pbsa/mm_pbsa_readinput.pm line 260, <IN>
> line
> > > 59.
> > > /usr/local/amber10/exe/sander -O -i pbsa_com.in -o
> pbsa_com.1.out
> > > -c
> > > ./snapshot_com.crd.1 -p ./com_vac.prmtop not successful
> > >
> > > I checked the mm_pbsa_readinput.pm, but don't know what I should do.
> > > Could
> > > anibody help me? Thank you.
> > >
> > >
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Bill Miller III
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-6715
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> >
> >
> > _______________________________________________
> > 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
>
>
>
>
> _______________________________________________
> 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
Received on Fri Oct 29 2010 - 12:30:04 PDT
