Hi James,
Try the AMBER14 manual.
Dump the raw values into .txt files and then run analysis using your favorite data analysis package.
I personally prefer R.
Parker
________________________________________
From: James Starlight [jmsstarlight.gmail.com]
Sent: Wednesday, February 18, 2015 5:53 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Distance/Angle distribution along the trajectory using cpptraj
Google has been crushed after I asked him about it!
Have fun,
James
2015-02-18 11:50 GMT+01:00 Nhai <nhai.qn.gmail.com>:
> Regarding the atom mask for dihedral angles, does google give you nothing?
>
> Hai
>
> > On Feb 18, 2015, at 4:51 AM, James Starlight <jmsstarlight.gmail.com>
> wrote:
> >
> > Dear Amber users!
> >
> > I'd like to calculate distribution of some value along the trajectory to
> > obtain its statistical distribution during the simulation. In my case
> the
> > calculated values are 1) distance between 2 atoms and 2) dihedral angle
> > which characterize rotation of some side-chain. I'd be thankful if
> someone
> > provide me with the cpptraj commands which can be used for such kind of
> the
> > analysis as well as amber-masks for the proper selection of the
> dihedrals.
> >
> > James
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
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Received on Wed Feb 18 2015 - 05:30:02 PST
