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.
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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Received on Thu Sep 29 2011 - 02:00:03 PDT
