On Fri, Apr 10, 2015 at 12:12 AM, Abhishek TYAGI <atyagiaa.connect.ust.hk>
wrote:
> Hi,
>
> I installed the MPI version of amber 14 according to the step 8 of the
> instruction of manual:
>
> cd $AMBERHOME
> ./configure -mpi <....other options....> <compiler-choice>
> make install
> # Note the value below may depend on your MPI implementation
> export DO_PARALLEL=”mpirun -np 2”
> make test
> # Note, some tests, like the replica exchange tests, require more
> # than 2 threads, so we suggest that you test with either 4 or 8
> # threads as well
> export DO_PARALLEL=”mpirun -np 8”
> make test
>
> As it reported error "mpi4py" not found, we built the mpi4py from the
> source code inside "Ambertools/src/mmpbsa_py".
>
> Then we tried to run:
> mpirun -np 4 /bin/MMPBSA.py.MPI -O -i mmpbsa.in -o out.dat -do out2.dat
> -sp solvated.prmtop -cp complex.prmtop -rp receptor.prmtop -lp
> ligand.prmtop -y last2.5ns.dcd
>
> The error said program "sander" not found.
> We checked the bin/ of amber, there is only sander.MPI NO sander.
> May I ask if we need to install serial version of amber before we
> configure and install MPI version in the same folder of amber 14?
>
Yes. As I said in my previous email, you need to install the serial
version of Amber to use MMPBSA.py.MPI. I suspect what you did was see that
sander and cpptraj were missing, so you just copied sander.MPI to sander
and cpptraj.MPI to cpptraj. As you saw, that clearly won't work.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Apr 10 2015 - 03:30:04 PDT
