From: Austin B. Yongye <>
Date: Fri, 25 Feb 2005 16:43:56 -0500 (EST)

Dear AMBER users,
I am trying to determine the pucker parameters 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
L0 7.552242e-02 2.292476e+01 4.929596e-01
L0 1.711139e-02 1.042250e+02 4.844757e-01
L0 1.149755e-01 3.181713e+02 4.895621e-01
L0 1.368749e-01 1.748987e+02 5.181410e-01
L0 4.004229e-02 2.029962e+02 5.764018e-01
L0 2.309195e-02 2.468739e+02 5.393260e-01
L0 4.703547e-03 8.509968e+01 5.157474e-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
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
 -73.028816 0.402920
 -78.079615 0.339020
 -58.075910 0.483107
 -66.928903 0.472729
 -69.442566 0.429326
 -72.610484 0.423635

Would be glad to have any explanations.

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Received on Fri Feb 25 2005 - 21:53:01 PST
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