Hi everybody,
so finally I get MMPBSA.py to work.GB calculation works fine but when
the PBSA calculation starts I get the following error:
Error: No potential terms in sander output! Check output files.
So I checked the *.mdout-Files. The ligand.mdout is fine but the
receptor and complex show this:
POST-PROCESSING OF TRAJECTORY ENERGIES
trajectory generated by ptraj
minimizing coord set # 1
SA Bomb in sa_arc(): Allocates aborted 0 0
1 0 0
I already tried to lower the fillratio which is mentioned in older
mailing list entrys but got the same error until I choosed
fillratio=1.0.Then I got this error:
POST-PROCESSING OF TRAJECTORY ENERGIES
trajectory generated by ptraj
minimizing coord set # 1
PB Bomb in setgrd(): focusing grid too large 2
automatically increased fillratio to 2.000
SA Bomb in sa_arc(): Allocates aborted 0 0
1 0 0
I really don't understand whats going wrong but maybe some of you
might have an idea. Thx in advance
Quoting Jason Swails <jason.swails.gmail.com>:
> You have to re-install MMPBSA.py in order to import the modules
> with the
> correct python version. Another option is just doing this by
> hand:
>
> cd $AMBERHOME/src/mmpbsa_py
> python2.7 -c "import alamdcrd inputparse utils"
> mv *.pyc ../../bin
>
> Good luck!
> Jason
>
> On Tue, Feb 22, 2011 at 11:16 AM, <poll.chemie.uni-hamburg.de>
> wrote:
>
> > Hi Jason,
> >
> > Thank you for these background informations. I installed
> python2.7 and
> > tried the MMPBSA.py again and still got the same error. Maybe it
> could
> > help to re-install the MMPBSA.py stuff?I'm using Amber11 so
> MMPBSA.py
> > is installed by default but maybe this went wrong.
> >
> > Quoting Jason Swails <jason.swails.gmail.com>:
> >
> > > Hello,
> > >
> > > Python 3.0 is basically a re-design of the python language.
> As
> > > such, code
> > > written in python2.x cannot be directly run with python3.x
> > > interpreter.
> > > There are many websites that detail this.
> > > http://wiki.python.org/moin/Python2orPython3 is one of them.
> For
> > > MMPBSA.py,
> > > you need to use either python2.6 or python2.7 (though this is
> > > changing in
> > > the upcoming release). In order to get it to work for
> python3.x,
> > > you have
> > > to pass each module and program through the "2to3" utility.
> Type
> > > "which
> > > 2to3" to verify that you have this program.
> > >
> > > However, you have an error that pops up before this becomes an
> > > issue, I made
> > > a comment below.
> > >
> > > On Tue, Feb 22, 2011 at 9:26 AM, <poll.chemie.uni-hamburg.de>
> > > wrote:
> > >
> > > > I tried to use MMPBSA.py.As mentioned in the manual a python
> > > version
> > > > 2.6 or later is needed. I used python3.0 which is already
> > > installed
> > > > on our machines. As I executed the MMPBSA.py I got the
> following
> > > > error:
> > > >
> > > > python3.0 $AMBERHOME/bin/MMPBSA.py
> > > >
> > > > Traceback (most recent call last):
> > > > File "/opt/amber11/bin/MMPBSA.py", line 44, in <module>
> > > > import inputparse, utils, alamdcrd # (2)
> > > > ImportError: Bad magic number in
> /opt/amber11/bin/inputparse.pyc
> > > >
> > >
> > > Just a little background to make this error make some sense:
> The
> > > first time
> > > a module is imported by python, the python interpreter
> "compiles"
> > > the module
> > > into what is called "byte-code", which is a binary .pyc file
> that
> > > loads
> > > faster than a text-based module. However, each version of
> python
> > > creates
> > > *different* byte-code binaries, so a .pyc file created with
> one
> > > version of
> > > python (i.e. python2.5) cannot be used with another version of
> > > python (i.e.
> > > python2.6, or python3.0, etc.). When you do try to import a
> .pyc
> > > file from
> > > a different version, it raises the exception you see
> (ImportError:
> > > Bad magic
> > > number). Try to find the default system python that compiled
> this
> > > version
> > > and use that (unless it's python < 2.6). The upcoming release
> will
> > > not be
> > > so finicky with regards to python version, and is a lot easier
> to
> > > install
> > > and run.
> > >
> > > Hope this helps,
> > > Jason
> > >
> > >
> > > > The script finds the inputparse.pyc but it seemed to be
> broken
> > > because
> > > > when I rename the inputparse.pyc I get
> > > >
> > > > Traceback (most recent call last):
> > > > File "/opt/amber11/bin/MMPBSA.py", line 44, in <module>
> > > > import inputparse, utils, alamdcrd # (2)
> > > > ImportError: No module named inputparse
> > > >
> > > > So the MMPBSA.py might not work with Python3.0?Any thoughts
> on
> > > this?
> > > >
> > > > Thx in advance
> > > >
> > > > Bernhard Poll
> > > >
> > > >
> > > > Quoting Jason Swails <jason.swails.gmail.com>:
> > > >
> > > > > Perhaps try using MMPBSA.py (
> > > > > http://ambermd.org/tutorials/advanced/tutorial3/py_script)
> > > instead.
> > > > > It may
> > > > > print out a more helpful error message if there is,
> indeed,
> > > one.
> > > > >
> > > > > Good luck,
> > > > > Jason
> > > > >
> > > > > On Thu, Feb 17, 2011 at 11:38 AM,
> <poll.chemie.uni-hamburg.de>
> > > > > wrote:
> > > > >
> > > > > > When I run this by hand no error occures and nothing
> strange
> > > in
> > > > > the
> > > > > > output-file. I tried to run the MMPBSA without this
> snapshot
> > > > > which
> > > > > > didn't work as well.
> > > > > >
> > > > > > Quoting steinbrt.rci.rutgers.edu:
> > > > > >
> > > > > > > Hi,
> > > > > > >
> > > > > > > > /opt/amber11/bin/sander -O -i pbsa_com.in -o
> > > > > > > pbsa_com.1.out -c
> > > > > > > > ./snapshot_com.crd.1 -p ./1q3w_out.prmtop not
> successfu
> > > > > > >
> > > > > > > this is the actual command that failed. You could run
> it
> > > by
> > > > > hand
> > > > > > > and see
> > > > > > > what the output says. pbsa can sometimes crash on
> unusual,
> > > > > large
> > > > > > > (or even
> > > > > > > random?) conformations, often the output file will
> contain
> > > an
> > > > > > > explanation
> > > > > > > or a suggestion of what parameter to change.
> > > > > > >
> > > > > > > In the worst case, you could do the MMPBSA analysis
> > > without
> > > > > data
> > > > > > > from that
> > > > > > > one problematic snapshot.
> > > > > > >
> > > > > > > Thomas
> > > > > > >
> > > > > > > Dr. Thomas Steinbrecher
> > > > > > > formerly at the
> > > > > > > BioMaps Institute
> > > > > > > Rutgers University
> > > > > > > 610 Taylor Rd.
> > > > > > > Piscataway, NJ 08854
> > > > > > >
> > > > > > > _______________________________________________
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> > > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > _______________________________________________
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> > > > > > AMBER.ambermd.org
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> > > > > >
> > > > >
> > > > >
> > > > >
> > > > > --
> > > > > Jason M. Swails
> > > > > Quantum Theory Project,
> > > > > University of Florida
> > > > > Ph.D. Candidate
> > > > > 352-392-4032
> > > > > _______________________________________________
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> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > >
> > > >
> > > >
> > > >
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> > > >
> > >
> > >
> > >
> > > --
> > > Jason M. Swails
> > > Quantum Theory Project,
> > > University of Florida
> > > Ph.D. Candidate
> > > 352-392-4032
> > > _______________________________________________
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> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> >
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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Feb 24 2011 - 02:30:04 PST
