Dear Dr. Jason and amber users,
Thank you very much for this help.
I had one more doubt.
Are the two versions of MMPBSA (ambertools 1.2 and ambertools 1.5) similar
and comparable?
That is: Can I compare the free energy values that I have calculated using a
combination of amber10 and MMPBSA.py script installed in ambertools 1.2 with
the ones that I will get using amber11 and ambertools 1.5?
Or is it better to repeat the MMPBSA calculation using latest version to
make realistic and meaningful comaprisons of binding free energies for
different ligands?
Thank you all.
On Tue, Aug 23, 2011 at 4:50 PM, Jason Swails <jason.swails.gmail.com>wrote:
> MMPBSA.py is now released with AmberTools 1.5. Also, to avoid python
> conflicts related to different versions being used to compile the modules
> and run the program, we replaced the MMPBSA.py and MMPBSA.py.MPI
> executables
> in $AMBERHOME/bin with shell scripts MMPBSA and MMPBSA.MPI that call the
> original program with the "appropriate" python.
>
> Thus, look for MMPBSA and MMPBSA.MPI and use those instead.
>
> Hope this helps,
> Jason
>
> On Tue, Aug 23, 2011 at 6:43 AM, vaibhav dixit <vaibhavadixit.gmail.com
> >wrote:
>
> > Dear Amber users,
> > I had earlier used amber10 earlier and had installed the MMPBSA.py script
> > for doing free energy calculations in AmberTools 1.2.
> >
> > Recently I have installed AmberTools 1.5 for using amber11.
> > But strangely the files necessary for performing MMPBSA calculations
> > (MMPBSA.py, utils.py, alamdcrd.py, and inputparse.py) are missing in the
> > folder /opt/amber11/bin. I could find the following python script instead
> > "ante-MMPBSA.py".
> >
> > There were no error messages while installing either AmberTools 1.5 or
> > amber11. A few last line are given below for the installation.
> >
> > Please help me troubleshoot why MMPBSA files are missing. Should I
> > reinstall
> > AmberTools and amber ?
> >
> > Thank you all.
> >
> >
> > AmberTool 1.5 installation
> > --------
> > mv AddToBox ChBox CheckMD PropPDB UnitCell /opt/amber11/bin
> > make[1]: Leaving directory
> `/opt/amber11/AmberTools/src/xtalutil/CPrograms'
> > (cd mmpbsa_py && make install)
> > make[1]: Entering directory `/opt/amber11/AmberTools/src/mmpbsa_py'
> > /bin/bash setup.sh
> > Using AmberTools' python
> > /opt/amber11/bin/nab -o mmpbsa_py_nabnmode mmpbsa_entropy.nab
> > /bin/mv mmpbsa_py_nabnmode /opt/amber11/bin
> > /opt/amber11/bin/nab -o mmpbsa_py_energy mmpbsa_energy.nab
> > /bin/mv mmpbsa_py_energy /opt/amber11/bin
> > make[1]: Leaving directory `/opt/amber11/AmberTools/src/mmpbsa_py'
> >
> > Installation of AmberTools, version 1.5 serial is complete at Tue Aug 23
> > 14:44:44 IST 2011.
> > ---------------
> >
> >
> >
> >
> > --
> > With regards
> >
> > Vaibhav A. Dixit
> > Ph.D. Scholar
> > Department of Medicinal Chemistry
> > Natl. Inst. Pharm. Edu. & Res. (NIPER)
> > Sector 67, Phase X, S.A.S. Nagar (Mohali)
> > Punjab -160 062 INDIA
> > Phone (Mobile): +919915214408
> > E-mail: vaibhavadixit.gmail.com
> > www.niper.nic.in
> > _______________________________________________
> > 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
>
--
With regards
Vaibhav A. Dixit
Ph.D. Scholar
Department of Medicinal Chemistry
Natl. Inst. Pharm. Edu. & Res. (NIPER)
Sector 67, Phase X, S.A.S. Nagar (Mohali)
Punjab -160 062 INDIA
Phone (Mobile): +919915214408
E-mail: vaibhavadixit.gmail.com
www.niper.nic.in
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Received on Tue Aug 23 2011 - 06:30:02 PDT
