Re: [AMBER] Xparmed.py

From: Arun Srikanth <askforarun.gmail.com>
Date: Wed, 24 Sep 2014 12:25:18 -0400

Thanks for the quick reply. Then, I have another question. Consider the
following example of methane

1 -C
2- H
3-H1
4-H2


now if you use

 printbonds.1 you get four bonds which is right.

if you try using printbonds .1-2 I was expecting 5 bonds to show up. Since
atom 2 is bonded to atom1 and atom 1 is bonded to all the four hydrogens.
but it is showing only four.

Is this right ?

Thanks
Arun


On Wed, Sep 24, 2014 at 12:05 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:

> '.1-2', '.1,2', and '.1@2' are equivalent.
>
> -Dan
>
> On Wed, Sep 24, 2014 at 9:58 AM, Arun Srikanth <askforarun.gmail.com>
> wrote:
> > 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
> >> _______________________________________________
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> >>
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>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
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Received on Wed Sep 24 2014 - 09:30:03 PDT
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