On Thu, Mar 26, 2015 at 1:59 AM, MOHD HOMAIDUR RAHMAN <rahmanhpu.gmail.com>
wrote:
> >
> > On Tue, Mar 24, 2015 at 3:31 AM, Subrata Paul <paul.subrata34.gmail.com>
>
> wrote:
>
> > Dear
>
> > Amber User,
>
> >
>
> > I have simulated a protein-urea-water system in AMBER12. Can we
> calculate
>
> > the vdw energy and electrostatic energy for water and urea around the
>
> > protein separately?
>
> > any hints ?
>
> >
>
> You can strip out the water using cpptraj and
> *compute the energy of each snapshot (using sander with imin=5).*
>
> Please elaborate this part how we are going to proceed this ? Similar to
> the normal MD (trajectory as input instead of rst file ) or any other step
> involves.
>
strip out the water using the "strip" command in cpptraj, with the
'outprefix' argument to write a new topology file that matches the system
you just printed out.
Then, compute the energy using sander. If you set the imin variable to 5,
you can provide an input trajectory file and calculate the energy of each
snapshot in that file.
Both of these commands are described in the Amber 14 manual, just look for
"strip" in the cpptraj chapter and "imin" in the sander chapter.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Mar 26 2015 - 07:30:03 PDT
