It's definitely possible to use them side-by-side. I think the page you're
referring to (
http://jswails.wikidot.com/installing-ambertools-12-and-older-amber)
details this combination and answers all of the questions you have.
HTH,
Jason
On Thu, Jun 7, 2012 at 12:49 AM, Adam Jion <adamjion.yahoo.com> wrote:
> Hi Jason,
>
> Thanks for the info. But is it possible for me to install AmberTools12
> whilst still using Amber11?
> I saw that your installation guide for installing AmberTools12 requires
> setting $AMBERHOME to 'amber12' directory.
> However, I'm currently using Amber11 and my $AMBERHOME points to 'amber11'.
> Will changing the $AMBERHOME path to 'amber12' directory still allow me to
> use Amber11?
> I ask this because of my previous nightmare making Amber11 work on my
> Ubuntu machine :-)
>
> Regards,
> Adam
>
> ------------------------------
> *From:* Jason Swails <jason.swails.gmail.com>
> *To:* AMBER Mailing List <amber.ambermd.org>
> *Sent:* Thursday, June 7, 2012 10:31 AM
> *Subject:* Re: [AMBER] Removing finite number of solvent particles from
> simulation box
>
> On Wed, Jun 6, 2012 at 10:31 PM, Jason Swails <jason.swails.gmail.com
> >wrote:
>
> >
> >
> > On Wed, Jun 6, 2012 at 9:12 PM, Adam Jion <adamjion.yahoo.com> wrote:
> >
> >> Hi!
> >>
> >> I need to remove a finite number of solvent particles from my simulation
> >> box after every 200 ns.
> >> Is it advisable to manually edit the .prmtop and .rst file?
> >> Or is there a better way using tleap?
> >>
> >
> > You can do it using parmed.py. See the "strip" command (xparmed.py will
> > not let you write out a restart file, parmed.py will).
> >
>
> Note, parmed.py is part of AmberTools 12
>
>
> >
> > HTH,
> > Jason
> >
> >
> >>
> >> Regards,
> >> Adam
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Jun 07 2012 - 07:30:03 PDT
