I installed Amber tools , as I intend to use MMPBSA I did the following steps,
cd $AMBERHOME/src/mmpbsa_py
make install
cd $AMBERHOME/test
make test mmpbsa_py
For example as in one of the tutorial :
$AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat
-sp err.solvated.prmtop -cp complex.prmtop -rp receptor.prmtop -lp
ligand.prmtop -y *.mdcrd
I could not find MMPBSA.py in $AMBERHOME/bin
I used as below (assuming the flags for -rp and -lp optional)
/home/amber11/AmberTools/src/mmpbsa_py/MMPBSA.py -O -i mmpbsa.in -o
FINAL_RESULTS_MMPBSA.dat -cp complex-vac.prmtop -y md_noWAT.x
VERSION: Command not found.
try:: Too many arguments.
It seems I did not install properly , please suggest.
Thanks
kirtana
On Fri, Sep 2, 2011 at 1:53 PM, Jason Swails <jason.swails.gmail.com> wrote:
> MMPBSA.py allows you to specify only a complex (so no receptor or ligand),
> and it will just give you the statistics for that one trajectory. If you
> cluster your simulations and collect "folded" and "unfolded" snapshots, then
> you can run MMPBSA.py on each of these clusters and get, roughly speaking,
> your free energy of folding. (Be aware of MMPBSA shortcomings, though).
>
> HTH,
> Jason
>
> On Fri, Sep 2, 2011 at 1:43 PM, KIRTANA S <skirtana4.gmail.com> wrote:
>
>> Hi Thomas,
>>
>> MMPBSA calculates the change in binding free energy of the ligand and
>> receptor.
>> How can I use this only for the complex only.
>>
>> Thanks
>> kirtana
>> Fri, Sep 2, 2011 at 2:43 AM, <steinbrt.rci.rutgers.edu> wrote:
>> > Hi Kirtana,
>> >
>> > you can use MM-PBSA for that purpose. There is a tutorial on how to use
>> it
>> > on the Amber page plus some examples in the $AMBERHOME/src/mmpbsa
>> > directory. But note that it will be very difficult to get the correct
>> > ensemble for your unfolded state.
>> >
>> > Kind Regards,
>> >
>> > Thomas
>> >
>> > On Thu, September 1, 2011 4:09 pm, KIRTANA S wrote:
>> >> I want to calculate the free energy change while my polymer folds.
>> >> I have used Implicit solvent, explicit solvent and also vacuum for my
>> >> simulation .
>> >>
>> >> How can I get the energy of the complex only throughout the simulation
>> >> run.
>> >>
>> >> Thanks in advance
>> >> kirtana
>> >>
>> >> _______________________________________________
>> >> AMBER mailing list
>> >> AMBER.ambermd.org
>> >> http://lists.ambermd.org/mailman/listinfo/amber
>> >>
>> >
>> >
>> > 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
>> >
>>
>> _______________________________________________
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>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Mon Sep 05 2011 - 14:00:08 PDT
