I use babel to convert a shelxl .res file to a PDB file. Actually, I don't mind having to fix my PDB files to conform (it doesn't happen that often) in order to have that H-bonding capability. I've attached a copy of the offending PDB file.
Pat
HEADER PROTEIN COMPND 3224.pdb AUTHOR GENERATED BY BABEL 1.6 ATOM 1 C 1 3.101 4.016 10.872 1.00 0.00 ATOM 2 C 1 4.604 4.193 10.226 1.00 0.00 ATOM 3 B 1 3.999 5.452 11.216 1.00 0.00 ATOM 4 B 1 3.087 4.597 12.473 1.00 0.00 ATOM 5 B 1 3.144 2.856 12.128 1.00 0.00 ATOM 6 B 1 4.099 2.616 10.651 1.00 0.00 ATOM 7 B 1 5.695 4.921 11.300 1.00 0.00 ATOM 8 B 1 4.742 5.166 12.787 1.00 0.00 ATOM 9 B 1 4.216 3.554 13.358 1.00 0.00 ATOM 10 B 1 4.841 2.325 12.221 1.00 0.00 ATOM 11 B 1 5.752 3.179 10.959 1.00 0.00 ATOM 12 B 1 5.832 3.752 12.635 1.00 0.00 ATOM 13 C 1 1.872 4.102 9.967 1.00 0.00 ATOM 14 H 1 1.749 3.239 9.543 1.00 0.00 ATOM 15 H 1 1.096 4.263 10.526 1.00 0.00 ATOM 16 C 1 1.899 5.145 8.898 1.00 0.00 ATOM 17 H 1 1.897 6.036 9.165 1.00 0.00 ATOM 18 C 1 1.925 4.896 7.599 1.00 0.00 ATOM 19 H 1 1.979 4.003 7.345 1.00 0.00 ATOM 20 C 1 1.877 5.900 6.500 1.00 0.00 ATOM 21 C 1 1.608 7.237 6.769 1.00 0.00 ATOM 22 H 1 1.422 7.508 7.639 1.00 0.00 ATOM 23 C 1 1.617 8.169 5.738 1.00 0.00 ATOM 24 H 1 1.437 9.063 5.917 1.00 0.00 ATOM 25 C 1 1.896 7.764 4.438 1.00 0.00 ATOM 26 H 1 1.902 8.387 3.747 1.00 0.00 ATOM 27 C 1 2.165 6.427 4.169 1.00 0.00 ATOM 28 H 1 2.352 6.156 3.299 1.00 0.00 ATOM 29 C 1 2.156 5.495 5.200 1.00 0.00 ATOM 30 H 1 2.336 4.600 5.021 1.00 0.00 ATOM 31 H 1 4.621 4.387 9.284 1.00 0.00 ATOM 32 H 1 3.672 6.381 10.755 1.00 0.00 ATOM 33 H 1 2.134 5.036 12.832 1.00 0.00 ATOM 34 H 1 2.258 2.272 12.249 1.00 0.00 ATOM 35 H 1 3.827 1.957 9.830 1.00 0.00 ATOM 36 H 1 6.453 5.589 10.877 1.00 0.00 ATOM 37 H 1 4.943 6.020 13.482 1.00 0.00 ATOM 38 H 1 4.061 3.323 14.417 1.00 0.00 ATOM 39 H 1 5.082 1.315 12.513 1.00 0.00 ATOM 40 H 1 6.542 2.759 10.300 1.00 0.00 ATOM 41 H 1 6.758 3.680 13.225 1.00 0.00 CONECT 1 2 3 4 5 6 13 CONECT 2 1 3 6 7 11 31 CONECT 3 1 2 4 7 8 32 CONECT 4 1 3 5 8 9 33 CONECT 5 1 4 6 9 10 34 CONECT 6 1 2 5 10 11 35 CONECT 7 2 3 8 11 12 36 CONECT 8 3 4 7 9 12 37 CONECT 9 4 5 8 10 12 38 CONECT 10 5 6 9 11 12 39 CONECT 11 2 6 7 10 12 40 CONECT 12 7 8 9 10 11 41 CONECT 13 1 14 15 16 CONECT 14 13 CONECT 15 13 CONECT 16 13 17 18 CONECT 17 16 CONECT 18 16 19 20 CONECT 19 18 CONECT 20 18 21 29 CONECT 21 20 22 23 CONECT 22 21 CONECT 23 21 24 25 CONECT 24 23 CONECT 25 23 26 27 CONECT 26 25 CONECT 27 25 28 29 CONECT 28 27 CONECT 29 20 27 30 CONECT 30 29 CONECT 31 2 CONECT 32 3 CONECT 33 4 CONECT 34 5 CONECT 35 6 CONECT 36 7 CONECT 37 8 CONECT 38 9 CONECT 39 10 CONECT 40 11 CONECT 41 12 MASTER 0 0 0 0 0 0 0 0 41 0 41 0 END
