[gmx-users] strange ffoplsaabon.itp adenine parameter

Malcolm Gillies malcolm.b.gillies at anu.edu.au
Tue Jul 22 09:06:01 CEST 2003

ffoplsaabon.itp contains the following dihedral parameter

  H      N2     CA     NC      3      2.93076  -2.93076   0.00000  
0.00000   0.00000   0.00000 ; Adenine RZ

this applies to the N1-C6-N6-HN6(1/2) dihedral in adenine. As far as I
know, this NH2 group is planar and coplanar with the heterocyclic ring,
meaning the dihedral should have minima at 0 and 180 degrees. This is in
fact the case for the other relevant dihedral parameter from this file:

  CB     CA     N2     H       3      8.49920   0.00000  -8.49920  
0.00000   0.00000   0.00000 ; aniline-like

(for C5-C6-N6-HN6(1/2))

As I don't know of the direct source for these parameters, I can't check
them. I also don't know what the "RZ" in the comment refers to.

Any suggestions? Are there original OPLS-AA parameter files I can get
for reference?

Thanks in advance.


Malcolm Gillies <Malcolm.B.Gillies at anu.edu.au>
Postdoctoral Fellow, Computational Proteomics and Therapy Design Group,
John Curtin School of Medical Research, Australian National University

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