Re: [AMBER] Xparmed.py

From: Jason Swails <jason.swails.gmail.com>
Date: Wed, 24 Sep 2014 11:04:42 -0400

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
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Received on Wed Sep 24 2014 - 08:30:02 PDT
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