Sourcing the ifortvars/iccvars scripts..!!!
Thanks and Regards,
Hirdesh
On Thu, Sep 29, 2011 at 7:23 PM, Jason Swails <jason.swails.gmail.com>wrote:
> 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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> > 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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Received on Thu Sep 29 2011 - 21:30:02 PDT
