Re: [AMBER] Xparmed.py

From: Arun Srikanth <askforarun.gmail.com>
Date: Wed, 24 Sep 2014 11:58:32 -0400

Also can you please explain the difference between .1-2 and @1.2 ?

On Wed, Sep 24, 2014 at 11:04 AM, Jason Swails <jason.swails.gmail.com>
wrote:

> On Wed, Sep 24, 2014 at 9:43 AM, Arun Srikanth <askforarun.gmail.com>
> wrote:
>
> > Hello.
> >
> > I have a question in xparmed.py.
> >
> > I am using the command printangles in xparmed.py
> >
> > I want to see only angles that contain both "1 and 2" with all the other
> > atoms.
>
>
> ​Neither ParmEd nor cpptraj supports this right now, although I've often
> wanted to do precisely this. I'll add this to the list of things to add to
> ParmEd.
>
> The best it can do is show you every angle that contains any of the atoms
> in the mask.
> ​
>
> > I am not sure how to set the mask for this
> >
> > .1-2 or @1.2 implements atom 1 or atom 2. But I want @1 and @2.
> >
>
> ​Your best bet is to supply just @1 or just @2 and then pick just the ones
> that have both atoms you want. printAngles @1 will print _every_ angle
> that contains atom 1, so it's guaranteed to also show any angles that
> include both atoms 1 and 2 if there are any. That is better than using
> .1-2, since that will show you more angles (i.e., those that include _only_
> atom 2).
>
> HTH,
> Jason
> ​
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> 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 Sep 24 2014 - 09:00:02 PDT
Custom Search