AMBER Archive (2008)

Subject: AMBER: launching a job works with sander.MPI and fail with pmemd.MPI

From: Thérèse Malliavin (
Date: Mon Dec 15 2008 - 08:41:55 CST

Dear AMBER Netters,

I have a question about the use of PMEMD. It is probably a trivial
question, but, as I did not find an answer neither on the Web pages
neither in the manuals, I am asking it to you.

I am doing the parallel calculations with sander.MPI using a lamd deamon
and the command nohup to launch the job, so I am doing:

. /Bis/shared/centos-3_x86_64/etc/custom.d/

before starting the AMBER calculations. The typical command line for
sander.MPI is then:

mpirun -np 4 ${AMBERHOME}/exe/sander.MPI -O -i -o mdr1.out -inf mdr1.inf -x mdr1.crd -c eq7.rst -p prmtop -r mdr1.rst

But, if I replace in the command line sander.MPI by pmemd.MPI:

mpirun -np 4 ${AMBERHOME}/exe/pmemd.MPI -O -i -o mdr1.out -inf mdr1.inf -x mdr1.crd -c eq7.rst -p prmtop -r mdr1.rst

I get an error saying that lamboot was not started.

I am trying to do these calculation on an 64 bits 8-proc Linux machine,
running under centos-3. The lam used is the version 7.1.2_intel-8.1.

Also, I am only using features which should exist in PMEMD according to
the AMBER manual.

Do you have any idea what I could check or what to find information to fix
this problem?

Thank you in abvance for your help,

Therese Malliavin
Unite de Bioinformatique Structurale
Institut Pasteur, Paris

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