You can set $AMBERHOME to the amber11 directory, or you can rename the nab
from AmberTools 1.2 to nab-1.2 or something and create a symbolic link from
AmberTools-1.4 version of nab into your amber10/bin directory. The last
option, and probably the best one, is to just build mmpbsa_py in the
amber11/src folder along with AmberTools-1.4.
Hope this helps,
Jason
On Sun, Sep 12, 2010 at 9:39 AM, Sangita Kachhap <sangita.imtech.res.in>wrote:
> Thanks for quick reply
>
> I have one confusion here I have installed amber10 with AmberTools-1.2
> now how I use AmberTools-1.4 for MMPBSA.py. installation?
>
>
> > Hello,
> >
> > There are a couple of problems here. First, the installation
> instructions
> > say that you need Python version 2.6 or higher (2.6 or 2.7 from python
> > website) in order to use MMPBSA.py. Also, you need to use nab from
> > AmberTools 1.4 in order to install the nmode program used by MMPBSA.py.
> >
> > Good luck!
> > Jason
> >
> > On Sun, Sep 12, 2010 at 6:59 AM, Sangita Kachhap <sangita.imtech.res.in
> >wrote:
> >
> >>
> >> Hello all
> >>
> >> I am installing python script for mm_pbsa in amber10.
> >> As instruction given in tutorial I have instralled mpi4py python module
> >> version
> >> mpi4py-1.2.1 in my home directory and my python version is Python 2.4.3
> it
> >> has
> >> installed successfully.
> >>
> >> To install python script
> >> I download it move it to $AMBERHOME/src directory and unpack it, move to
> >> unpacked
> >> directory and typed make serial installation end with following error :
> >>
> >> make serial
> >> /bin/bash setup.sh
> >> Python version 2 detected. No file conversion necessary.
> >> /bin/cp MMPBSA.py *pyc /home/sangita/amber10/bin
> >> /home/sangita/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/sangita/amber10/bin
> >> /bin/mv: cannot stat `mmpbsa_py_nabnmode': No such file or directory
> >> make: [install] Error 1 (ignored)
> >>
> >> In my unpacked directory there was not such file when I checked it.
> >> So what I should do to install it.
> >>
> >>
> >> With regard
> >> Sangita Kachhap
> >> JRF
> >> BIC,IMTECH
> >> CHANDIGARH
> >>
> >> _______________________________________________
> >> 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
> >
> >
>
>
> Sangita Kachhap
> JRF
> BIC,IMTECH
> CHANDIGARH
>
> _______________________________________________
> 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
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AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Sep 12 2010 - 07:30:03 PDT
