He, Yang wrote:
Hi all users,
I just encountered a problem about the DNA model when I set the coordinate in
the pdb file . It always shows very strange figure about the DNA model.
My pdb file is like this:
ATOM 1 Ab1 DNA 1 0.051 0.575 0.516 1.0 0.0
ATOM 2 Tb1 DNA 1 0.191 0.159 2.344 1.0 0.0
ATOM 3 S1 DNA 1 1.280 2.365 6.568 1.0 0.0
ATOM 4 S2 DNA 1 1.280 -2.365 -6.568 1.0 0.0
ATOM 5 P1 DNA 1 2.186 -0.628 8.896 1.0 0.0
ATOM 6 P2 DNA 1 2.186 -0.628 -8.896 1.0 0.0
ATOM 7 S3 DNA 1 4.660 -1.947 6.704 1.0 0.0
ATOM 8 S4 DNA 1 4.660 1.947 -6.704 1.0 0.0
ATOM 9 Cb1 DNA 1 3.431 0.162 0.756 1.0 0.0
ATOM 10 Gb1 DNA 1 3.571 -1.249 1.989 1.0 0.0
ATOM 11 P3 DNA 1 5.556 -5.737 6.828 1.0 0.0
ATOM 12 P4 DNA 1 5.556 5.737 -6.828 1.0 0.0
ATOM 13 S5 DNA 1 8.040 -5.516 4.279 1.0 0.0
ATOM 14 S6 DNA 1 8.040 5.516 -4.279 1.0 0.0
ATOM 15 Gb2 DNA 1 6.811 -1.814 1.407 1.0 0.0
ATOM 16 Cb2 DNA 1 6.951 -0.319 0.764 1.0 0.0
ATOM 17 P5 DNA 1 8.936 -8.655 2.152 1.0 0.0
ATOM 18 P6 DNA 1 8.936 8.655 -2.152 1.0 0.0
ATOM 19 S7 DNA 1 11.42 6.978 0.220 1.0 0.0
ATOM 20 S8 DNA 1 11.42 -6.978 -0.220 1.0 0.0
ATOM 21 Tb2 DNA 1 10.191 -0.707 0.430 1.0 0.0
ATOM 22 Ab2 DNA 1 10.331 -2.237 -0.518 1.0 0.0
CONECT 1 3
CONECT 2 4
CONECT 3 1 5
CONECT 4 2 6
CONECT 5 3 7
CONECT 6 4 8
CONECT 7 5 9 11
CONECT 8 6 10 12
CONECT 9 7
CONECT 10 8
CONECT 11 7 13
CONECT 12 8 14
CONECT 13 11 15 17
CONECT 14 12 16 18
CONECT 15 13
CONECT 16 14
CONECT 17 13 19
CONECT 18 14 20
CONECT 19 17 21
CONECT 20 18 22
CONECT 21 19
CONECT 22 20
MASTER 0 0 0 0 0 0 0 0 22 0 22 0
END
Can anyone of you tell me whether there is something wrong with my pdb file?
Your atom names look more like you have a bizarre cluster of sulfur and
heavy atoms, not DNA. Also possible is that you have a united-atom model
with about one site per nucleic acid residue. I've no idea whether any
united-atom models of DNA exist.
Mark
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