AMBER Archive (2005)

Subject: Re: AMBER: Pyranose pucker parameters

From: Thomas E. Cheatham, III (cheatham_at_chpc.utah.edu)
Date: Wed Apr 27 2005 - 22:57:26 CDT

On Sat, 26 Feb 2005, Austin B. Yongye wrote:

> I am trying to determine the pucker parameters of neuraminic acid from an
> MD, using the Cremer and Pople convention.
> First, I used carnal and got some output which I couldn't relate to the
> pucker parameters. Here are the first 8 lines of my output:
>
> L0 1.766151e-01 2.044298e+02 6.147423e-01
...
>
> I think the third column represents the pucker amplitude. The middle
> column looks like phi/psi. But some of the numbers in the column are above
> 180deg.
> Would be glad to know what these columns represent.
> Secondly, when I used ptraj with the same Cremer et al convention, I got
> different numbers. Here are the first 8 lines from my ptraj output:
> Pseudorot Amplitude
> -52.048026 0.542751
> -83.469735 0.406082

OK, I finally got around to using the pucker routines myself again...

By default, ptraj uses the Altona&Sundaringam conventions which is
slightly different than the Cremer&Pople and offset by 90.0 degrees.

To reproduce carnal numbers for standard nucleic acid sugars, I use in
ptraj:

pucker p1 :1_at_C1' :1_at_C2' :1_at_C3' :1_at_C4' :1_at_O4' out p1.dat cremer offset -90.0

By default, ptraj will do the Altona; the differences are ~1-2 degrees.

If ptraj is doing what you would like, make sure you are choosing the
correct atoms for the ring...

As far as carnal is concerned, that pucker table produced is dumped in the
form amplitude pucker amplitude pucker ...

L0 1.766151e-01 2.044298e+02 6.147423e-01
L0 7.552242e-02 2.292476e+01 4.929596e-01

So the first amplitude dumped as 204 deg, ...

A carnal expert like Bill Ross my have further comment.

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