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
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Received on Wed Apr 22 2015 - 11:00:05 PDT
