Hi All,
I am checking dihedral parameters using rdparm for my LNA
tetranucleotide, and here are some results from rdparm's dihedral
command:
for force field A:
269: 0.000 0.00 2.0 :1.C2' :1.C1' :1.N1 :1.C2 (24,8,10,20)
357: 0.000 0.00 2.0 :2.O4' :2.C1' :2.N9 :2.C4 (39,40,42,55)
443: 0.000 0.00 2.0 :3.O4' :3.C1' :3.N9 :3.C4 (73,74,76,89)
512: 0.000 0.00 2.0 :4.C2' :4.C1' :4.N1 :4.C2 (123,108,110,119)
for force field B:
251: 0.000 0.00 2.0 :1.C2 :1.N1 :1.C1' :1.O4' (20,10,8,7)
367: 0.000 0.00 2.0 :2.O4' :2.C1' :2.N9 :2.C4 (39,40,42,55)
458: 0.000 0.00 2.0 :3.O4' :3.C1' :3.N9 :3.C4 (73,74,76,89)
514: 0.000 0.00 2.0 :4.C2 :4.N1 :4.C1' :4.O4' (119,110,108,107)
The two molecules are identical except for the force fields.
Unfortunately the AMBER manual said nothing about how to read the
output. I thought that the four numbers at right were atom #s, but
the two molecules are identical. My question is, what are the 3
numbers on the left? I thought they were cosine terms but then the
different force fields are giving vastly different results, as they
were designed to.
What are the 4 numbers on the right?
thanks in advance for your time,
-Dave
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Received on Tue Apr 19 2011 - 10:00:04 PDT
