the best way is to read Amber14 manual first.
http://ambermd.org/doc12/Amber14.pdf (page 571)
Hai
On Wed, Apr 22, 2015 at 1:47 PM, Atila Petrosian <atila.petrosian.gmail.com>
wrote:
> Dear Jason
>
> Thanks for your attention.
>
> If I install only AmberTools14, can I use sander for MM-PBSA and MM-GBSA
> calculation?
>
>
> On Wed, Apr 22, 2015 at 3:35 PM, Jason Swails <jason.swails.gmail.com>
> wrote:
>
> > On Wed, Apr 22, 2015 at 12:18 AM, Atila Petrosian <
> > atila.petrosian.gmail.com
> > > wrote:
> >
> > > Dear Jason
> > >
> > > Thanks for your answer
> > >
> > >
> > >
> > > I don’t have Amber 14 license, then based on your suggestion, I will
> use
> > > AmberTools 14 includes sander. Now, I have 3 questions:
> > >
> > >
> > > 1) Is pmemd needful for sander and md simulation. Can’t I use sander in
> > > AmberTools 14 without pmemd? Please give me more explanation about the
> > > importance of pmemd.
> > >
> >
> > pmemd gives the same answers as sander and only has a small subset of
> > sander's functionality (e.g., it does not do QM/MM, EVB, PIMD, LCOD
> > restraints, chemical shift restraints, NOESY restraints, etc.). But it
> > runs substantially faster. On CPUs, it's ~2x faster and scales better on
> > parallel hardware. On GPUs, it's ~10x faster still.
> >
> >
> > >
> > > 2) Is there any instruction for installation of AmberTools 14 on CentoS
> > > 6.3?
> > >
> >
> > Installation is the same for basically all distros -- the only thing
> that
> > differs is *how* to install the prerequisites. CentOS is in the same
> > family as Fedora and Red Hat, so follow the fedora instructions here:
> > http://ambermd.org/ubuntu.html
> >
> >
> > > 3) Already, I had installed AmberTools 14 Ubuntu 11.04 using this link:
> > >
> > > http://bgamari.github.io/posts/2011-10-16-amber.html
> > >
> > >
> > > <http://bgamari.github.io/posts/2011-10-16-amber.html>
> > >
> > > you said, sander is included in AmberTools 14. How to use sander in
> > > AmberTools 14? Using following command?
> > >
> > >
> > > $AMBERHOME/exe/sander -O -i *.in -o *.out -p *.prmtop -c *.inpcrd -r
> > *.rst
> > >
> >
> > $AMBERHOME/exe has not existed for many years. It is $AMBERHOME/bin
> now.
> > But that general command works.
> >
> > I suggest going through some of the Tutorials, which will likely help you
> > get started (especially tutorial B0) at http://ambermd.org/tutorials/
> >
> > HTH,
> > Jason
> >
> > --
> > Jason M. Swails
> > BioMaPS,
> > Rutgers University
> > Postdoctoral Researcher
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Wed Apr 22 2015 - 11:00:05 PDT
