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!
________________________________
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
Received on Thu Nov 04 2010 - 07:00:02 PDT
