Hi Marcos,
it is working now, I also had to make exectuable all the run files- don't
know why.
However, I really thank you for helping , and spending your time.
Best Regards
Il giorno gio 27 set 2018 alle ore 15:53 Marcos Serrou do Amaral <
marcossamaral.gmail.com> ha scritto:
> Hi Emanuele,
> You need to change
> system("qsub run.pbs.$dihed"); to
> system("./run.$dihed.sh");
>
> Good luck!
>
>
> On Thu, Sep 27, 2018, 10:15 emanuele falbo <falbo.emanuele.gmail.com>
> wrote:
>
> > Hi Marcos,
> >
> > I tried as you said, unfortunately it doesn't work. I got these two error
> > messages when submitting the script:
> >
> > "
> > Name "main::wd" used only once: possible typo at
> > ./prepare_runs_0-90-modified.perl line 3.
> > Preparing input files
> > Processing dihedral: 0
> > Can't exec "qsub": No such file or directory at
> > ./prepare_runs_0-90-modified.perl line 27.
> > Processing dihedral: 3
> > "
> >
> > The "Can't exec .." is repeated for all runs till dihe=90. ( here is the
> > files modified)
> >
> > Do you think I should change the qsub command when preparing the input
> > files, if so how ?
> >
> > Note I simply renamed ala_tri.rst file with 03_prod_60. Your help is
> > really appreacited.
> >
> > Emanuele
> >
> >
> >
> >
> > Il giorno gio 27 set 2018 alle ore 14:56 emanuele falbo <
> > falbo.emanuele.gmail.com> ha scritto:
> >
> > > thanks for promptly replying Marcos.
> > > I will give it a try and then let you know. Thanks again.
> > >
> > > Cheers,
> > > Emanuele
> > >
> > > Il giorno gio 27 set 2018 alle ore 14:52 Marcos Serrou do Amaral <
> > > marcossamaral.gmail.com> ha scritto:
> > >
> > >> Dear Emanuele,
> > >>
> > >> You could try to change the write_batchfile function and try something
> > >> like
> > >> this:
> > >>
> > >> sub write_batchfile {
> > >> open BATCHFILE, '>', "run.$dihed.sh";
> > >> print BATCHFILE <<EOF;
> > >>
> > >> #!/bin/bash
> > >>
> > >> mpirun -np 2 pmemd.MPI -O \\
> > >> -i mdin_min.$dihed -p ${name}.prmtop -c ala_tri_prod_60.rst -r
> > >> ${name}_min_${dihed}.rst -o ${name}_min_${dihed}.out
> > >> mpirun -np 2 pmemd.MPI -O \\
> > >> -i mdin_equi.$dihed -p ${name}.prmtop -c ${name}_min_${dihed}.rst -r
> > >> ${name}_equil_${dihed}.rst -o ${name}_equil_${dihed}.out
> > >> mpirun -np 2 pmemd.MPI -O \\
> > >> -i mdin_prod.$dihed -p ${name}.prmtop -c ${name}_equil_${dihed}.rst -r
> > >> ${name}_prod_${dihed}.rst -o ${name}_prod_${dihed}.out -x
> > >> ${name}_prod_${dihed}.mdcrd
> > >> EOF
> > >>
> > >> print BATCHFILE "\necho \"Execution finished\"\n";
> > >> close BATCHFILE;
> > >> }
> > >>
> > >> Good luck!
> > >> ---
> > >> Marcos S.A.
> > >>
> > >>
> > >>
> > >> On Thu, Sep 27, 2018 at 9:34 AM emanuele falbo <
> > falbo.emanuele.gmail.com>
> > >> wrote:
> > >>
> > >> > Dear users,
> > >> >
> > >> > I am following the umbrella sampling tutorial on the web site
> > >> > http://ambermd.org/tutorials/advanced/tutorial17/section2.htm .
> > >> > I got a bit stuck when using the perl scripts for running all the
> > >> > calculations., because I would like to use these scripts (here is
> > >> attached
> > >> > one type.) for running the calculations in parallel on my
> workstation
> > >> ( it
> > >> > is not a cluster).
> > >> >
> > >> > So , I am wondering if anybody knows the way to modify them and get
> > the
> > >> > calculations done successfully.
> > >> >
> > >> > Best Regards
> > >> >
> > >> >
> > >> >
> > >> > --
> > >> >
> > >> > *Emanuele Falbo*
> > >> > PhD student
> > >> > Penfold group
> > >> > School of Natural and Environmental Sciences
> > >> > Bedson Building, Newcastle University
> > >> > Newcastle upon Tyne, NE1 7RU
> > >> > w: http://tompenfoldresearch.weebly.com/
> > >> > _______________________________________________
> > >> > AMBER mailing list
> > >> > AMBER.ambermd.org
> > >> > http://lists.ambermd.org/mailman/listinfo/amber
> > >> >
> > >> _______________________________________________
> > >> AMBER mailing list
> > >> AMBER.ambermd.org
> > >> http://lists.ambermd.org/mailman/listinfo/amber
> > >>
> > >
> > >
> > > --
> > >
> > > *Emanuele Falbo*
> > > PhD student
> > > Penfold group
> > > School of Natural and Environmental Sciences
> > > Bedson Building, Newcastle University
> > > Newcastle upon Tyne, NE1 7RU
> > > w: http://tompenfoldresearch.weebly.com/
> > >
> > >
> >
> > --
> >
> > *Emanuele Falbo*
> > PhD student
> > Penfold group
> > School of Natural and Environmental Sciences
> > Bedson Building, Newcastle University
> > Newcastle upon Tyne, NE1 7RU
> > w: http://tompenfoldresearch.weebly.com/
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
*Emanuele Falbo*
PhD student
Penfold group
School of Natural and Environmental Sciences
Bedson Building, Newcastle University
Newcastle upon Tyne, NE1 7RU
w: http://tompenfoldresearch.weebly.com/
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Received on Thu Sep 27 2018 - 12:00:02 PDT
