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
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Mon May 24 2010 - 23:30:04 PDT
