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
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Received on Tue Aug 23 2011 - 04:30:03 PDT
