If you want to do NEB simulations, I strongly suggest using Amber11. NEB was
completely rewritten and is much more straightforward to use now.
On Fri, Aug 20, 2010 at 8:06 AM, Jason Swails <jason.swails.gmail.com>wrote:
> Hi Cat,
>
> You say NED, something I'm unfamiliar with, but then your input files say
> neb. Are you doing Nudged Elastic Band simulations? If so, there's a
> tutorial that should provide the help you need: tutorial A5.
> http://ambermd.org/tutorials/advanced/tutorial5
>
> Hope this helps,
> Jason
>
> On Fri, Aug 20, 2010 at 5:39 AM, Catein Catherine <askamber23.hotmail.com
> >wrote:
>
> >
> > Dear Sir/Madam,
> >
> >
> >
> > I would like to run NED in amber10. I found sander.PIMD was used in
> > tutorial 5 for amber9. As no sander.PIMD can be found in my
> AMBERHOME/exe
> > directory, I cannot run this job as in the tutorial.
> >
> >
> >
> > AMBERHOME/exe/sander.PIMD -O -i md-ala-neb-smallk_1.in -o
> > md-ala-neb-smallk_1.out -p neb.prmtop -c neb.inpcrd -r
> > md-ala-neb-smallk_1.rst -x md-ala-neb-smallk_1.mdcrd
> >
> >
> >
> > so, I tried to submit the job as follows by using sander.MPI. However,
> it
> > did not works. The file stop by complaining that "Flags: MPI ***This
> > version will not accept topology files that were created by addles, with
> > NPARM=1 use a version compiled with -DLES"
> >
> >
> >
> > AMBERHOME/exe/sander.MPI -O -i md-ala-neb-smallk_1.in -o
> > md-ala-neb-smallk_1.out -p neb.prmtop -c neb.inpcrd -r
> > md-ala-neb-smallk_1.rst -x md-ala-neb-smallk_1.mdcrd
> >
> >
> >
> > >From the archive, some report the use of sander.LES.MPI, so I also give
> it
> > a try. I submit the job in tutorial 5, section 4 as follows, but The
> > output file stop at weight changes/NMR restraints.
> >
> >
> >
> > AMBERHOME/exe/sander.MPI -O -i md-ala-neb-smallk_1.in -o
> > md-ala-neb-smallk_1.out -p neb.prmtop -c neb.inpcrd -r
> > md-ala-neb-smallk_1.rst -x md-ala-neb-smallk_1.mdcrd
> >
> >
> >
> > Could you mind to let me know how to run the NED in amber10?
> >
> >
> >
> > Best regards,
> >
> >
> >
> > Cat
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Aug 20 2010 - 09:30:03 PDT
