Hi Bin,
You should keep replying on the mailing list, since I also get those emails
and you get the full benefit of the whole community that way.
On Thu, Nov 4, 2010 at 2:45 AM, bin wang <wang_p_z.yahoo.com.cn> wrote:
> Hello Dr. Swails,
> I applied the bug fixes and recompiled AMBER 10, then run the mm_pbsa
> test. But the same error still showed up.
> I have been stuck in this binding energy calculation for a long time. I am
> trying to install MMPBSA.py but it hasn't work out yet. Could you give me
> more suggestion on this problem?
> Thank you very much!
>
Until I know what you tried, and how it failed, the only thing I can tell
you is to follow the instructions on
http://ambermd.org/tutorials/advanced/tutorial3/py_script/compile.htm
Good luck,
Jason
>
>
> Best,
> Bin
>
> ------------------------------
> *From:* Jason Swails <jason.swails.gmail.com>
> *To:* AMBER Mailing List <amber.ambermd.org>
> *Sent:* Fri, October 29, 2010 4:16:44 PM
> *Subject:* Re: [AMBER] Error message from binding_energy.mmpbsa
>
> If the tests don't run, then you can't expect it to work in the *real
> world*. You should apply the mm_pbsa bug fixes and recompile.
>
> Another option is to try MMPBSA.py, available on
> ambermd.org/tutorials/advanced/tutorial3/py_script . You'll have to spend
> some time/effort getting it installed (don't forget to apply patches if you
> choose to use that version).
>
> Good luck!
> Jason
>
> On Fri, Oct 29, 2010 at 4:10 PM, bin wang <wang_p_z.yahoo.com.cn> wrote:
>
> > I run make in my $AMBERHOME/src/mm_pbsa/Examples, it showed errors:
> >
> >
> > cd 01_GenerateSnapshots; /exe/mm_pbsa.pl mm_pbsa.in > mm_pbsa.log 2>&1
> > make: *** [test.GenerateSnapshots] Error 127
> >
> > What can I do next?
> >
> >
> >
> >
> >
> > ________________________________
> > From: Jason Swails <jason.swails.gmail.com>
> > To: AMBER Mailing List <amber.ambermd.org>
> > Sent: Fri, October 29, 2010 3:17:18 PM
> > Subject: Re: [AMBER] Error message from binding_energy.mmpbsa
> >
> > 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
> >
> >
> >
> >
> > _______________________________________________
> > 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
>
>
--
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 Thu Nov 04 2010 - 05:00:06 PDT
