It was suggested in a previous thread (
http://archive.ambermd.org/201006/0490.html) that this error is not due to a
fillratio issue, but instead to the fact that you do not have enough memory
to run the calculation. You can either try running the calculation on a
system with more memory, or try adjusting the arcres variable, as the thread
previously mentioned suggests.
Good luck!
-Bill
On Thu, Feb 24, 2011 at 5:27 AM, <poll.chemie.uni-hamburg.de> wrote:
> 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
> > > > > > > >
> > > > > > > > _______________________________________________
> > > > > > > > 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. Candidate
> > > > > > 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. Candidate
> > > > 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. Candidate
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
>
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>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Thu Feb 24 2011 - 04:00:09 PST
