On 27 May 2014 15:19, Jason Swails <jason.swails.gmail.com> wrote:
> On Tue, May 27, 2014 at 9:04 AM, Massimiliano Porrini <
> m.porrini.iecb.u-bordeaux.fr> wrote:
>
> > On 26 May 2014 21:21, Jason Swails <jason.swails.gmail.com> wrote:
> >
> > > One other comment I'll make is that you can actually have ParmEd run
> > OpenMM
> > > simulations for you directly. There is an "OpenMM" command that
> behaves
> > > exactly like sander -- it reads sander/pmemd input files, runs a
> > > calculation with OpenMM, and writes sander-formatted trajectories and
> > > restart files. You would use this command exactly the same way as you
> > > would run sander or pmemd on the command-line.
> > >
> > > $ parmed.py -p my.prmtop
> > > loadRestrt my.inpcrd
> > > OpenMM -O -i mdin -o mdout -x mdcrd -i mdinfo ...etc
> > >
> > > This may make it a bit easier to use OpenMM coming from an Amber
> > > background.
> > >
> >
> > I assume this is only available in Amber14, like you had already
> mentioned
> > it in a previous
> > email of yours. And in my group unfortunately we do not have Amber14...
> >
>
> This is actually in AmberTools 14 -- freely available under an open source
> license. It should (hopefully) be easy enough to install. (And again, you
> can download and install ParmEd separately if you wish to keep up-to-date
> with the OpenMM-related developments).
>
Alright, apparently I am a bit slow today... flu effects!
And actually I have already installed AT14 in my computer, I'll have a look
at it, thanks.
Max
>
> All the best,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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>
--
Dr Massimiliano Porrini
Valérie Gabelica Team
U869 ARNA - Inserm / Bordeaux University
Institut Européen de Chimie et Biologie (IECB)
2, rue Robert Escarpit
33607 Pessac Cedex
FRANCE
Tel : 33 (0)5 40 00 63 31
http://www.iecb.u-bordeaux.fr/teams/GABELICA
Emails: m.porrini.iecb.u-bordeaux.fr
mozz76.gmail.com
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Received on Tue May 27 2014 - 07:00:03 PDT
