Hi,
I don't quite understand how your system works. Do you not have a
submission scrip with the sander command inside? Or do you have to
give the whole "sander -O ..." directly from some sort of command
line?
Gustavo.
On Wednesday, June 16, 2010, vaibhav wrote:
> 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 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
> _______________________________________________
> 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
Received on Wed Jun 16 2010 - 02:30:10 PDT
