What version of AmberTools are you using?
-Bill
On Tue, May 25, 2010 at 1:56 AM, Rilei Yu <yulaomao1983.yahoo.com.cn> wrote:
> Hi, everyone who may concern this letter,
>
> When I installed the updated script, the error appears as follows:
>
> r.yu.euphoria:~/amber10/src/mmpbsa_py$ make serial
> /bin/bash setup.sh
> Python version 2 detected. No file conversion necessary.
> /bin/cp MMPBSA.py *pyc /home/r.yu/amber10/bin
> /home/r.yu/amber10/bin/nab -o mmpbsa_py_nabnmode mmpbsa_entropy.nab
> mmpbsa_entropy.nab:58 fld 'ls_method' not in struct 'xo'
> mmpbsa_entropy.nab:58 operator '=': left operand has wrong class.
> mmpbsa_entropy.nab:58 unknown attribute 'ls_method'
> mmpbsa_entropy.nab:59 fld 'ls_maxiter' not in struct 'xo'
> mmpbsa_entropy.nab:59 operator '=': left operand has wrong class.
> mmpbsa_entropy.nab:59 unknown attribute 'ls_maxiter'
> mmpbsa_entropy.nab:60 fld 'ls_maxatmov' not in struct 'xo'
> mmpbsa_entropy.nab:60 operator '=': left operand has wrong class.
> mmpbsa_entropy.nab:60 unknown attribute 'ls_maxatmov'
> nab2c failed!
> make: [install] Error 1 (ignored)
> /bin/mv mmpbsa_py_nabnmode /home/r.yu/amber10/bin
> /bin/mv: cannot stat `mmpbsa_py_nabnmode': No such file or directory
> make: [install] Error 1 (ignored)
>
> Can anyone give me suggestions please?
>
> Best Regards,
>
> Rilei Yu
>
> --- 10年5月25日，周二, Jason Swails <jason.swails.gmail.com> 写道：
>
> 发件人: Jason Swails <jason.swails.gmail.com>
> 主题: Re: FW: [AMBER] MMPBSA.py update
> 收件人: "AMBER Mailing List" <amber.ambermd.org>
> 日期: 2010年5月25日,周二,上午9:07
>
> On Mon, May 24, 2010 at 8:39 PM, Beroza, Paul <Paul.Beroza.elan.com>
> wrote:
>
> >
> > How do we obtain the new release of mmpbsa.py?
> >
>
> The source code is found in the second link provided in the release email:
>
> source code can be obtained along with the installation instructions on
> this site (ambermd.org/tutorials/advanced/tutorial3/py_script/compile.htm
> ).
>
> If you have any more questions, please feel free to ask.
>
> Good luck!
> Jason
>
>
> > Thanks, Paul
> >
> > -----Original Message-----
> > From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On
> > Behalf Of Jason Swails
> > Sent: Monday, May 24, 2010 3:53 PM
> > To: AMBER Mailing List
> > Subject: [AMBER] MMPBSA.py update
> >
> > Hello,
> >
> > My co-authors and I are pleased to announce the release of an update to
> > MMPBSA.py. This is a significant update with many improvements and
> > additions. I will briefly describe the improvements and additions,
> > though they can be found in more detail in the RELEASE_NOTES.txt
> > included with the new source code.
> >
> > Improvements and additions:
> > - Normal mode calculations are done completely within a nab program
> > - MPI has been implemented directly in python script, improving
> > parallelization
> > - Decomposition analysis (both per-residue and pairwise) implemented
> > - Ability to rewrite outputs without re-doing calculations
> > - More extensive test suite
> > - Improved error catching and messages
> > - Fixed many bugs in infrequently tested calculations
> >
> > This version, last updated around 5/21/2010, is even more recent than
> > the version released recently with Amber11, so we encourage people that
> > plan to use this script to upgrade to the new version. Old input files
> > should continue to work except for the two changes mentioned below. All
> > common calculations are discussed in detail in the tutorial for
> > MMPBSA.py (
> > ambermd.org/tutorials/advanced/tutorial3/py_script/index.htm). The
> > source code can be obtained along with the installation instructions on
> > this site (
> > ambermd.org/tutorials/advanced/tutorial3/py_script/compile.htm).
> >
> > Changes:
> > - initial_traj variable was changed to strip_mdcrd (more informative
> > name). See manual.
> > - mpi_cmd and nproc were removed as variables due to new MPI
> > implementation
> >
> > Thanks!
> > Jason, Dwight, and Bill
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > ********************************************************
> > This communication and any files transmitted with it
> > may contain information that is confidential, privileged
> > and exempt from disclosure under applicable law. It is
> > intended solely for the use of the individual or entity
> > to which it is addressed. If you are not the intended
> > recipient, you are hereby notified that any use,
> > dissemination or copying of this communication is
> > strictly prohibited. If you have received this
> > communication in error, please notify the sender.
> > Thank you for your co-operation.
> > ********************************************************
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 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
Received on Tue May 25 2010 - 05:00:43 PDT
