AMBER Archive (2007)

Subject: Re: AMBER: use of pucker function in ptraj

From: Thomas Cheatham III (tec3_at_utah.edu)
Date: Thu May 10 2007 - 11:48:58 CDT

> I'm new to amber and seemed to have a problem with the pucker
> function. A simulation of A-DNA (DNA duplex d(CCAACGTTGG)2 ) at 300K was
> ran using amber for 1ns with each frame being 2ps. I'm currently trying
> to analyze the results, especially the pucker change. A-Dna should
> transit to resemble a state close to B-DNA and have its pucker value
> change from 18 to 162 degrees.

Realistically, the pucker should change (assuming low salt, solvated),
however the various AMBER parm9X force fields tend to underestimate the
B-DNA pucker provided average values closer to 120-130 deg for parm94 and
higher for parm98/99.

However, I think your input to ptraj is messed up...

> ptraj dna.top << EOF
> trajin md1.crd
> pucker puck :1_at_C1' :3_at_C2' :3_at_C3' :1_at_C4' :1_at_O4' out dnapuck.dat

Usually you want the pucker on a single residue, not between multiple
residues as above, i.e.

   pucker puck :1_at_C1' :1_at_C2' :1_at_C3' :1_at_C4' :1_at_O4' out dnapuck.dat

In addition, pucker alone is not sufficient to characterize A- vs. B- DNA;
likely you will want to look at helicoidal parameters and other indicators
of similarity to A- or B-

--tec3
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