Re: [AMBER] Question about ptraj artifacts

From: Kamali Sripathi <ksripath.umich.edu>
Date: Wed, 27 Apr 2011 11:52:26 -0400

Hi Jason,

I'm very sorry for my long delay in replying. Thank you very much for the
information.

On Sun, Apr 24, 2011 at 1:11 PM, Jason Swails <jason.swails.gmail.com>wrote:

> On Wed, Apr 20, 2011 at 1:06 PM, Kamali Sripathi <ksripath.umich.edu>
> wrote:
> you no longer have a function (i.e., -181 degrees and 179 degrees are the
> same angle, yet both
> are within your range!)
>
> This is actually what I often see, so sometimes it's difficult for me to
tell which angle (i.e, -181º or 179º) is the real dihedral angle.


>
> The line "Y = Y < -100 ? Y + 360 : Y" literally means "if Y is less than
> -100, then add 360 to it, otherwise leave it alone". This, therefore
> defines a range [-100, 260) for the angles. Adjust this as necessary for
> your use case.
>
>
This is what I've ended up doing, actually. Sometimes when it's not clear
whether I should define the range as, e.g., <-100 or > 100, I try both, and
see which looks more reasonable. This not be the best way to do things, but
it makes the most sense to me.

Thanks again for your response, Jason, and have a great day,

Kamali
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Received on Wed Apr 27 2011 - 09:00:05 PDT
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