> 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.C1' :3.C2' :3.C3' :1.C4' :1.O4' out dnapuck.dat
Usually you want the pucker on a single residue, not between multiple
residues as above, i.e.
pucker puck :1.C1' :1.C2' :1.C3' :1.C4' :1.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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Received on Sun May 13 2007 - 06:07:26 PDT
