Actually we have amber10 installed on a HPC cluster where we can access it
only through a portal which allows to submit only sander jobs. So I'm
looking for a method to link all the sander (min, heat, density and equil)
jobs in one sander input where I can give initial prmtop and inpcrd files
and the jobs can run sequentially.
Please find time and see if you can suggest some solution to the same.
Thanks in advance...
On Tue, Jun 15, 2010 at 4:30 PM, Gustavo Seabra <gustavo.seabra.gmail.com>wrote:
> How about making a shell script and submitting the script instead?
>
> Gustavo.
>
> On Tuesday, June 15, 2010, vaibhav dixit wrote:
> > 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
> > www.niper.nic.in
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
> --
> Gustavo Seabra
> Professor Adjunto
> Departamento de Química Fundamental
> Universidade Federal de Pernambuco
> Fone: +55-81-2126-7417
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
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
www.niper.nic.in
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Received on Wed Jun 16 2010 - 02:00:03 PDT
