On Thu, Sep 29, 2011 at 4:54 AM, Hirdesh Kumar <hirdesh.science.gmail.com>wrote:
> Hi Jason,
> Thank you for your suggestion. I have solved the issue as per ur suggestion
> and happy to add that I have successfully completed the tutorial.
>
Which one? Sourcing the ifortvars/iccvars scripts or recompiling with GNU?
>
> Thank you for your support.
>
> Hirdesh
>
> On Thu, Sep 29, 2011 at 11:06 AM, Jason Swails <jason.swails.gmail.com
> >wrote:
>
> > On Thu, Sep 29, 2011 at 12:47 AM, Hirdesh Kumar
> > <hirdesh.science.gmail.com>wrote:
> >
> > > Hi All,
> > > I am trying to run MMPBSA job on Amber11 with AT1.5. For starting I
> tried
> > > to
> > > follow the given tutorial at the Amber homepage. I copied all the
> > required
> > > files and put them in a folder..
> > > The files are:
> > > 1err_prod.mdcrd 1err.solvated.prmtop complex.prmtop ligand.prmtop
> > > mmpbsa.in receptor.prmtop
> > >
> > > When I tried to run command
> > > * /opt/amber11/amber11/exe/MMPBSA.MPI -O -i mmpbsa.in -o
> > > FINAL_RESULTS_MMPBSA.dat -sp 1err.solvated.prmtop -cp complex.prmtop
> -rp
> > > receptor.prmtop -lp ligand.prmtop -y *.mdcrd*
> > >
> > > I got following error message:
> > > Running MMPBSA.MPI on 1 processors...
> > > Reading command-line arguments and input files...
> > > Loading and checking parameter files for compatibility...
> > > ptraj found! Using /opt/amber11/amber11/bin/ptraj
> > > mmpbsa_py_energy found! Using /opt/amber11/amber11/bin/mmpbsa_py_energy
> > for
> > > GB calculations
> > > mmpbsa_py_energy found! Using /opt/amber11/amber11/bin/mmpbsa_py_energy
> > for
> > > PB calculations
> > > Preparing trajectories for simulation...
> > > 50 frames were read in and processed by ptraj for use in calculation.
> > >
> > > Beginning GB calculations with mmpbsa_py_energy...
> > > calculating complex contribution...
> > > calculating receptor contribution...
> > > calculating ligand contribution...
> > >
> > > Beginning PB calculations with mmpbsa_py_energy...
> > > calculating complex contribution...
> > > PB Info in pb_read(): npopt has been overwritten with inp
> > > */opt/amber11/amber11/bin/mmpbsa_py_energy: symbol lookup error:
> > > /opt/amber11/amber11/bin/mmpbsa_py_energy: undefined symbol:
> > > __svml_sincos2*
> > >
> > > Please suggest me how to get rid of this issue.
> > >
> >
> > It looks like you used the intel compilers to build Amber (including nab)
> > and linked dynamically. As a result, your LD_LIBRARY_PATH still needs to
> > be
> > populated with the directory containing the basic Intel compiler
> libraries
> > (in this case, libsvml.a or something). The intel compilers typically
> ship
> > with a script that automatically loads necessary environment variables.
> > For
> > my system, with my version of the Intel compilers (using
> bash/ksh/dash/sh),
> > I use the command
> >
> > source /opt/intel/Compiler/11.1/069/bin/ifortvars.sh intel64
> >
> > Note that your system may differ slightly, but you get the basic idea.
> You
> > should put this command somewhere in your .bashrc or other resource file
> > that is sourced automatically (or something similar).
> >
> > Another option is to just recompile Amber and AmberTools with the GNU
> > compilers, which will avoid this altogether.
> >
> > HTH,
> > Jason
> >
> >
> > >
> > > Thanks and Regards,
> > > Hirdesh Kumar
> > > _______________________________________________
> > > 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Sep 29 2011 - 07:00:02 PDT
