Hi Jason,
Thanks a lot! I guess I'll probably use an awk script to do it.
Yuan
On Wed, Mar 23, 2011 at 6:35 PM, Jason Swails <jason.swails.gmail.com>wrote:
> Hello,
>
> ptraj cannot do this. You can write a nab program that will do this if you
> want. You can also use sander with imin=5, and just take the VDW energies.
> This is easily automated with an awk script (or with a simple perl or
> python script). There's no utility that will take a trajectory and *just*
> dump van der waals energies (unless you write it yourself).
>
> Hope this helps,
> Jason
>
> On Wed, Mar 23, 2011 at 5:41 PM, Yuan Ding <uscchem.gmail.com> wrote:
>
> > Hi Amber users,
> > I'm new to Amber, and I have a question about energy extraction. Is there
> a
> > way to extract only the vdw energy of a structure and print it out in a
> > separate text file by ptraj? I realized the output file of minimization
> > includes a list of all kinds of energy, but since I have a lot of
> > structures
> > to look at, I can't check the vdw energy one by one. If ptraj can't do
> it,
> > can other tools of Amber serve the same purpose?
> > Thank you in advance for the help!
> > Yuan
> > _______________________________________________
> > 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Mar 23 2011 - 19:00:03 PDT
