Re: [AMBER] Xparmed.py

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Wed, 24 Sep 2014 10:05:15 -0600

'.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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-- 
-------------------------
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 - 09:30:02 PDT
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