I see. It seems that I have to use python. But I still don't know why the
mm_pbsa.pl doesn't work in my computer.
Thank you.
________________________________
From: Jason Swails <jason.swails.gmail.com>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Thu, November 4, 2010 9:52:30 AM
Subject: Re: [AMBER] Error message from binding_energy.mmpbsa
I did include my answer with the last email you sent me, but inside the body
of the email. See below for my comments:
On Thu, Nov 4, 2010 at 9:49 AM, bin wang <wang_p_z.yahoo.com.cn> wrote:
> 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?
>
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
> Thank you very much!
>
>
>
> ________________________________
> From: Jason Swails <jason.swails.gmail.com>
> To: bin wang <wang_p_z.yahoo.com.cn>; AMBER Mailing List <
> amber.ambermd.org>
> Sent: Thu, November 4, 2010 7:49:21 AM
> Subject: Re: [AMBER] Error message from binding_energy.mmpbsa
>
> 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
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
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AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
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Received on Thu Nov 04 2010 - 12:00:03 PDT
