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Hi Xiangjun
I am having trouble with XYZ files converted to PDB format using OpenBabel, the XYZ files come from gaussian 09 optimised structures. Whenever I try using the converted PDB file with find_pair, I always get the message that there are no base pairs. The converted files open normally in viewers like avogadro, so I don't think there should be any issues from the conversion process. I see a similar topic was raised (Conversions, jterry0402) but not pursued. I have attached both the original and converted files.
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Hi Kyle,
As shown in the attached image, your PDB file does not have proper atoms naming for the nucleotides. Specifically, atoms in your OpenBabel converted PDB file are simply named C, N, O for base, sugar and the phosphate. A section of your PDB file is listed below.
HETATM 1 C UNK 1 2.399 -4.315 -0.508 1.00 0.00 C
HETATM 2 O UNK 1 1.582 -4.309 0.656 1.00 0.00 O
HETATM 3 C UNK 1 2.481 -2.904 -1.056 1.00 0.00 C
HETATM 4 O UNK 1 1.218 -2.500 -1.603 1.00 0.00 O
HETATM 5 C UNK 1 2.845 -1.853 -0.001 1.00 0.00 C
HETATM 6 O UNK 1 3.660 -0.873 -0.641 1.00 0.00 O
HETATM 7 C UNK 1 1.485 -1.297 0.415 1.00 0.00 C
HETATM 8 C UNK 1 0.639 -1.443 -0.851 1.00 0.00 C
HETATM 9 N UNK 1 -4.340 -0.429 -1.822 1.00 0.00 N
HETATM 10 C UNK 1 -3.213 0.196 -2.239 1.00 0.00 C
HETATM 11 N UNK 1 -1.952 -0.117 -1.914 1.00 0.00 N
HETATM 12 C UNK 1 -1.870 -1.170 -1.108 1.00 0.00 C
HETATM 13 C UNK 1 -2.957 -1.913 -0.612 1.00 0.00 C
HETATM 14 C UNK 1 -4.215 -1.480 -1.014 1.00 0.00 C
HETATM 15 N UNK 1 -2.509 -2.950 0.192 1.00 0.00 N
HETATM 16 C UNK 1 -1.209 -2.829 0.175 1.00 0.00 C
HETATM 17 N UNK 1 -0.752 -1.767 -0.583 1.00 0.00 N
HETATM 18 P UNK 1 4.328 0.338 0.255 1.00 0.00 P
HETATM 19 C UNK 1 2.724 2.003 -0.968 1.00 0.00 C
HETATM 20 O UNK 1 3.104 1.437 0.279 1.00 0.00 O
HETATM 21 C UNK 1 1.430 2.759 -0.796 1.00 0.00 C
HETATM 22 O UNK 1 0.387 1.842 -0.466 1.00 0.00 O
HETATM 23 C UNK 1 1.426 3.850 0.313 1.00 0.00 C
HETATM 24 O UNK 1 1.219 5.147 -0.230 1.00 0.00 O
HETATM 25 C UNK 1 0.209 3.484 1.163 1.00 0.00 C
HETATM 26 C UNK 1 -0.597 2.602 0.209 1.00 0.00 C
HETATM 27 N UNK 1 -1.539 1.692 0.839 1.00 0.00 N
HETATM 28 C UNK 1 -2.880 1.786 0.508 1.00 0.00 C
HETATM 29 O UNK 1 -3.338 2.618 -0.262 1.00 0.00 O
HETATM 30 N UNK 1 -3.678 0.857 1.137 1.00 0.00 N
3DNA (and DSSR/SNAP) requires standard names for a nucleotide to be recognized -- see Fig.1 of the 2015 DSSR NAR paper (https://doi.org/10.1093/nar/gkv716). Check a RCSB PDB entry (see below), e.g., 355d (http://www.rcsb.org/pdb/explore/explore.do?structureId=355d), you will see how the atoms are named:
ATOM 17 P DG A 2 23.337 31.278 21.156 1.00 13.26 P
ATOM 18 OP1 DG A 2 24.761 31.571 21.391 1.00 13.17 O
ATOM 19 OP2 DG A 2 22.651 31.834 19.956 1.00 12.34 O
ATOM 20 O5' DG A 2 23.180 29.714 21.092 1.00 12.20 O
ATOM 21 C5' DG A 2 23.830 28.894 22.040 1.00 10.87 C
ATOM 22 C4' DG A 2 23.663 27.461 21.627 1.00 10.59 C
ATOM 23 O4' DG A 2 22.328 27.016 21.920 1.00 10.81 O
ATOM 24 C3' DG A 2 23.866 27.232 20.130 1.00 11.75 C
ATOM 25 O3' DG A 2 24.412 25.926 20.055 1.00 16.36 O
ATOM 26 C2' DG A 2 22.447 27.195 19.590 1.00 10.31 C
ATOM 27 C1' DG A 2 21.722 26.527 20.744 1.00 8.31 C
ATOM 28 N9 DG A 2 20.293 26.737 20.884 1.00 6.86 N
ATOM 29 C8 DG A 2 19.536 27.799 20.464 1.00 7.02 C
ATOM 30 N7 DG A 2 18.276 27.683 20.786 1.00 7.92 N
ATOM 31 C5 DG A 2 18.201 26.464 21.447 1.00 5.72 C
ATOM 32 C6 DG A 2 17.091 25.790 22.018 1.00 5.63 C
ATOM 33 O6 DG A 2 15.916 26.151 22.052 1.00 7.25 O
ATOM 34 N1 DG A 2 17.464 24.566 22.588 1.00 4.99 N
ATOM 35 C2 DG A 2 18.749 24.064 22.600 1.00 4.83 C
ATOM 36 N2 DG A 2 18.930 22.867 23.187 1.00 6.47 N
ATOM 37 N3 DG A 2 19.786 24.688 22.072 1.00 6.26 N
ATOM 38 C4 DG A 2 19.440 25.872 21.516 1.00 6.25 C
HTH,
Xiang-Jun
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Thanks, that does confirm what I had suspected. However I still don't have a way to create the correct PDB format from XYZ files. I suppose I could try change the file manually but that doesn't seem like an efficient way to do things, given this is something I will have to do many times. Is there a function in 3DNA that will do this? Or is there a program other than openbabel that does the conversion properly?
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3DNA does not have a tool to perform such auto coversions. I vaguely remember Babel could do a better job in some cases, from 3DNA users. Check the openbabel community, and let us know what you find.
An the end of th day, only you know your system well. It may be feasible to write a script/program to convert your .XYZ to .PDB efficiently, taking consideration of standard naming convention of the A/C/G/T/U bases.
Xiang-Jun
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I found the problem, mainly that I was working with mutated bases. It is still possible, but first you need to modify the file so it only contains the four canonical bases before running it through babel. Otherwise it doesn't recognise the molecule as DNA and just creates a generic PDB file.