[AMBER] how can i run min.in heat.in density.in equil.in as one sander job?

From: vaibhav dixit <vaibhavadixit.gmail.com>
Date: Tue, 15 Jun 2010 15:45:58 +0530

Dear Amber community members,

I'm running MD simulations on a set of proteins (72 pdb structures known for
my target).

Here I use procedure given in tutorial
<http://ambermd.org/tutorials/advanced/tutorial3/section1.htm>to run min.in,
heat.in, density.in and equil.in jobs one after the other on cluster through
portal that we have here. Followed by production phase of the calculation.

Is there any possibility where I can modify the input so that all these jobs
will run one after the other (like link jobs) instead having to submit
them separately?

One issue is that the portal is adding some extra numbers in the last line
of the restart file, which I have to remove manually before submitting the
next job, else the job fails. Will this fact affect any such attempts to
link these jobs?

This linking of jobs will save time once prmtop and inpcrd files are
prepared from the pdb.

Please find time and see if you can suggest some solution for the same.

Thank you all in advance and waiting for reply...

With regards
Vaibhav A. Dixit
Ph.D. Scholar
Department of Medicinal Chemistry
Natl. Inst. Pharm. Edu. & Res. (NIPER)
Sector 67, Phase X,  S.A.S. Nagar (Mohali)
Punjab -160 062 INDIA
Phone (Mobile): +919915214408
E-mail: vaibhavadixit.gmail.com
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Received on Tue Jun 15 2010 - 03:30:03 PDT
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