[AMBER] Re: FW: Requesting your help in amber

From: Jenny Iskrenova <jnova2001.gmail.com>
Date: Tue, 8 Jun 2010 09:04:22 -0400

Dear Subha,

You should send your questions to the AMBER mailing list as other people may
run into similar problems and may find the discussions and your experience
helpful, the same way as you found my name and e-mail from the mailing list.

The error that you are getting:
line 12: ...
is what it says -- there is no file "sander.PIMD.MPI" in the specified
After loading the AMBER module you could try:

echo $AMBERHOME <-- this will tell you where the AMBER
installation is

and you will see where the amber binary file is and what it is called on
your machine.

As for the script, the way it is written, there will be a problem. You may
want to talk to the help staff on the supercomputer for details specific to
that machine. There should be some example scripts that would show you how
to submit a job to the queue on your machine. You may also want to consult
some introductory books on Unix/Linux.

In the script, try adding this line before invoking sander:


where $PBS_O_WORKDIR is a variable that holds the name of the work
directory -- the variable name will depend on how it was set on your

Also, if you want to run a parallel version of the codes, you would have to
run the MPI binary and you would have to use something like:

mpirun -np 4 $AMBERHOME/exe/sander.MPI .....

Hope this gets you started!

Jenny Iskrenova

On Mon, Jun 7, 2010 at 8:49 PM, subha k <subhali24.gmail.com> wrote:

> Dear Jenny Iskrenova,
> Good day!
> I use a pbs script to run amber 10 module. I have attached the
> script.FYI,Tango is the supercomputer name.
> I have run several examples from amber tutorial, everything went on well.
> But, as far as the NEB simulated annealing example, I get different errors.
> When I use "*$AMBERHOME/exe/sander.PIMD.MPI*" as mentioned in the
> tutorial, I get the below error.
> */usr/spool/PBS/mom_priv/jobs/987839.tango-m.vpac.org.SC: line 12:
> /usr/local/amber/10-openmpi-gcc/exe/sander.PIMD.MPI: No such file or
> directory*
> So, I tried , "*$AMBERHOME/exe/sander*", i get the below error,
> *Unit 5 Error on OPEN: md-ala-neb_300K_equil.in *
> Could not understand, why this happens.
> Can you pls help me in this?
> Many Thanks and Best Regards,
> Subha
> On Tue, Jun 8, 2010 at 12:26 AM, Jenny Iskrenova <jnova2001.gmail.com>wrote:
>> Dear Subha,
>> What is the exact error message? Could you, please, provide more
>> information on how exactly you are submitting the run on the supercomputers?
>> It could be that there is some problem in the script that you are using.
>> Jenny Iskrenova
>> ________________________________________
>> From: subha k [subhali24.gmail.com]
>> Sent: Monday, June 07, 2010 3:24 AM
>> To: Jenny Iskrenova
>> Subject: Requesting your help in amber
>> Dear Jenny Iskrenova,
>> Good Day!
>> I am Ms.Subha, a PhD researcher at La trobe University,Australia. I
>> recently saw your reply in the amber forum for the post on "Unit 5 error on
>> open" in amber. I get the same error when i tried the amber example(tutorial
>> 7-section 5). Could you please help me in solving this error?
>> I have placed all the files in the same working directory but, still i
>> receive the same error for both the inputs.I have also attached the files
>> for you. FYI,I am using amber from a supercomputer.
>> Expecting your early favourable reply,
>> Many Thanks,
>> Subha
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Received on Tue Jun 08 2010 - 06:30:03 PDT
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