AMBER Archive (2007)

Subject: AMBER: QMMM simulations

From: Pankaj R. Daga (pdaga_at_olemiss.edu)
Date: Tue Nov 27 2007 - 17:20:51 CST

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 min.in -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
below.

 

 

****************************************

Initial min of our structure QMMM

 &cntrl

  imin=1, maxcyc=500, ncyc=200,

  cut=8.0, ntb=1, ntc=1, ntf=1,

  ifqnt=1

 /

 &qmmm

  qmmask=':410-412',

  qmcharge=3,

  spin = 2

  qmtheory=1,

  qmshake=1,

  qm_ewald=1, qm_pme=1

 /

 

****************************************

 

Please help me a way out.

 

Thanks and Regards

 

Pankaj

 

===================================================================
If your ship doesn't come in, swim out to it.......Jonathan Winters
===================================================================
Pankaj R. Daga |
Department of Medicinal Chemistry | e-mail: pdaga_at_olemiss.edu
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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