You will have to use the -write-mdins flag when running MMPBSA.py to write
out the necessary input files for the calculation. Then, edit the input(s)
for PB calculations by adding or placing arcres=0.125 in the &pb section of
the input file. Finally, re-run the MMPBSA.py calculation, but add the
-use-mdins flag so that the script uses your altered input file(s) instead
of creating a new one(s).
-Bill
On Thu, Feb 24, 2011 at 8:09 AM, <poll.chemie.uni-hamburg.de> wrote:
> Some (maybe stupid) questition.Where can I adjust the arcres?In my
> input-file?When I put arcres=0.125 into my mmpbsa.in the program
> tolds that this is an invalid option.
>
> Thank you.
>
> Bernhard Poll
>
> Quoting Bill Miller III <brmilleriii.gmail.com>:
>
> > 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
> > > >
> > >
> > >
> > >
> > >
> > > _______________________________________________
> > > 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
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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 - 18:30:04 PST
