What version of AmberTools are you using? The installation is failing when
trying to compile the entropy code, which is a nab program. You will need to
be using the nab from AmberTools 1.4 or later in order for this to compile
correctly. AmberTools 1.4 opens into an amber11 directory tree, and since
the nab that is being used to compile here is in an amber10 directory
(/vol5/home/cadd/amber/amber10/bin/nab), then I am going to guess this is
your problem. You will either need to download and install AmberTools 1.4
from the Amber website, or if you have already done that, make sure that
your environment is setup so that the the AmberTools 1.4 is used instead of
nab from Amber10.
Good luck!
-Bill
On Fri, Apr 8, 2011 at 4:38 AM, fancy2012 <fancy2012.yeah.net> wrote:
> Dear amber users,
>
> I meet a problem when I install MMPBSA.py on my computer. Here are the
> process of installation and errors:
>
> Before I compile it, I apply the patches first. But I guess that the
> patching is failed, just as showed like this:
> patching file src/mmpbsa_py/MMPBSA.py
> patching file src/mmpbsa_py/MMPBSA.py.MPI
> patching file src/mmpbsa_py/mmpbsa_entropy.nab
> patching file src/mmpbsa_py/Makefile
> Reversed (or previously applied) patch detected! Skipping patch.
> 1 out of 1 hunk ignored -- saving rejects to file
> src/mmpbsa_py/Makefile.rej
> patching file src/mmpbsa_py/utils.py
> patching file src/mmpbsa_py/MMPBSA.py.MPI
> Hunk #1 succeeded at 1020 (offset -3 lines).
> patching file src/mmpbsa_py/utils.py
> Hunk #1 FAILED at 4.
> 1 out of 4 hunks FAILED -- saving rejects to file
> src/mmpbsa_py/utils.py.rej
>
>
> So when I ran make serial in mmpbsa_py, it failed. Here are the errors:
>
> /bin/bash setup.sh
> Python version 2 detected. No file conversion necessary.
> /bin/cp MMPBSA.py *pyc /vol5/home/cadd/amber/amber10/bin
> /vol5/home/cadd/amber/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 /vol5/home/cadd/amber/amber10/bin
> /bin/mv: cannot stat `mmpbsa_py_nabnmode': No such file or directory
> make: [install] Error 1 (ignored)
>
>
> >From the above lines, I guess it is the problem of patching, so could
> someone tell me how to figure it out? Any response will be highly
> appreciated. Thanks!
> --
> Best wishes,
>
> Qinghua
>
> Ph.D student of Tianjin University, China
> _______________________________________________
> 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
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Received on Fri Apr 08 2011 - 04:30:05 PDT
