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
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Sep 28 2011 - 23:00:03 PDT
