AMBER: QMMM simulations

From: Pankaj R. Daga <>
Date: Tue, 27 Nov 2007 17:20:51 -0600

Hi amber community,


I am trying to run one amber QMMM simulation using sander. When I run
minimization using single processor, the job runs fine. However, when I
submit the job using multiple processors, I get the error as shown below.




mpirun -np 4 /usr/local/appl/amber9/exe/sander.MPI -O -i -o
1rtd_min1.out -p 1rtd_box.prmtop -c 1rtd_box.inpcrd -r 1rtd_min.rst7


/usr/local/appl/amber9/exe/sander.MPI: symbol lookup error:
/usr/local/appl/amber9/exe/sander.MPI: undefined symbol: ?0_memcopyA

MPI: MPI_COMM_WORLD rank 0 has terminated without calling MPI_Finalize()

MPI: aborting job




The installation of amber9 was proper and According to Amber test results,
Amber 9 is functioning properly for single and multiple cpus. Could anybody
help me to figure out, where is the problem? The input file is as shown




Initial min of our structure QMMM


  imin=1, maxcyc=500, ncyc=200,

  cut=8.0, ntb=1, ntc=1, ntf=1,






  spin = 2



  qm_ewald=1, qm_pme=1





Please help me a way out.


Thanks and Regards




If your ship doesn't come in, swim out to it.......Jonathan Winters
Pankaj R. Daga |
Department of Medicinal Chemistry | e-mail:
417 Faser Hall, School of Pharmacy | fax: +1-662-915-5638
University of Mississippi | phone: +1-662-915-1853
University, MS, 38677-1848 |


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Received on Wed Nov 28 2007 - 06:07:42 PST
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