Hello,
i’m trying to use Haddock2.2 to compute electrostatic energy in order to use in Prodigy-ligand web service.
My complex is a protein/phospholipid (PC) but PRODRG is finding unusual geometry:
PRODRG> Molecule complexity index: 2.07.
PRODRG> 0 explicit hydrogen(s) added.
PRODRG> 29 bonds 11 ambiguous
PRODRG> 42 bond angles 16 ambiguous
PRODRG> C9 has unusual geometry. Check coordinates!
Is haddock can deal with phospholipid ?
Thanks,
BR,
Emmanuel
Yes it can - define it as HETATM (if you are using the web server)
Already done !
Here is my PC lines:
HETATM 3903 C8 PC5 B 601 39.831 22.898 3.883 1.00 4.98 PC_e C
HETATM 3904 H8 PC5 B 601 39.625 21.834 3.902 1.00 7.42 PC_e H
HETATM 3905 C9 PC5 B 601 38.511 23.606 3.520 1.00 6.82 PC_e C
HETATM 3906 1H9 PC5 B 601 37.720 23.182 4.101 1.00 9.74 PC_e H
HETATM 3907 2H9 PC5 B 601 38.577 24.639 3.781 1.00 8.44 PC_e H
HETATM 3908 O6 PC5 B 601 38.199 23.481 2.140 1.00 9.95 PC_e O
HETATM 3909 C10 PC5 B 601 38.003 23.370 1.403 1.00 45.61 PC_e C
HETATM 3910 O7 PC5 B 601 38.149 23.353 1.799 1.00144.18 PC_e O
HETATM 3911 C11 PC5 B 601 37.597 23.265 0.009 1.00 39.01 PC_e C
HETATM 3912 1H11 PC5 B 601 37.575 23.299 -0.280 1.00 56.52 PC_e H
HETATM 3913 2H11 PC5 B 601 37.561 23.180 -0.180 1.00 63.52 PC_e H
HETATM 3914 C12 PC5 B 601 37.264 23.230 -0.754 1.00106.99 PC_e C
HETATM 3915 1H12 PC5 B 601 37.323 23.228 -0.494 1.00188.53 PC_e H
HETATM 3916 2H12 PC5 B 601 37.298 23.282 -0.605 1.00178.72 PC_e H
HETATM 3917 C13 PC5 B 601 36.800 23.129 -2.054 1.00108.88 PC_e C
HETATM 3918 1H13 PC5 B 601 36.707 23.118 -2.284 1.00116.04 PC_e H
HETATM 3919 2H13 PC5 B 601 36.762 23.121 -2.250 1.00123.73 PC_e H
HETATM 3920 C14 PC5 B 601 36.518 23.060 -2.790 1.00221.94 PC_e C
HETATM 3921 1H14 PC5 B 601 36.423 23.136 -3.034 1.00283.60 PC_e H
HETATM 3922 2H14 PC5 B 601 36.417 23.014 -2.885 1.00303.31 PC_e H
HETATM 3923 3H14 PC5 B 601 36.499 22.968 -3.022 1.00287.26 PC_e H
HETATM 3924 O5 PC5 B 601 40.822 23.145 2.861 1.00 4.36 PC_e O
HETATM 3925 C15 PC5 B 601 41.379 24.344 2.566 1.00 3.25 PC_e C
HETATM 3926 O8 PC5 B 601 41.324 25.337 3.268 1.00 3.15 PC_e O
HETATM 3927 C16 PC5 B 601 42.171 24.284 1.283 1.00 5.83 PC_e C
HETATM 3928 1H16 PC5 B 601 42.881 25.085 1.248 1.00 7.27 PC_e H
HETATM 3929 2H16 PC5 B 601 42.727 23.381 1.273 1.00 10.09 PC_e H
HETATM 3930 C17 PC5 B 601 41.303 24.318 0.055 1.00 10.25 PC_e C
HETATM 3931 1H17 PC5 B 601 41.018 23.643 -0.160 1.00 33.50 PC_e H
HETATM 3932 2H17 PC5 B 601 40.691 24.718 0.162 1.00 35.08 PC_e H
HETATM 3933 C18 PC5 B 601 41.625 24.701 -1.033 1.00 24.41 PC_e C
HETATM 3934 1H18 PC5 B 601 41.809 25.337 -0.883 1.00 62.18 PC_e H
HETATM 3935 2H18 PC5 B 601 42.233 24.391 -1.076 1.00 60.34 PC_e H
HETATM 3936 C19 PC5 B 601 40.890 24.633 -2.269 1.00 25.91 PC_e C
HETATM 3937 1H19 PC5 B 601 40.747 24.646 -2.599 1.00 59.17 PC_e H
HETATM 3938 2H19 PC5 B 601 40.662 24.643 -2.564 1.00 52.18 PC_e H
HETATM 3939 3H19 PC5 B 601 40.699 24.563 -2.590 1.00 58.32 PC_e H
HETATM 3940 C7 PC5 B 601 40.319 23.280 5.298 1.00 4.61 PC_e C
HETATM 3941 1H7 PC5 B 601 40.467 24.335 5.354 1.00 7.36 PC_e H
HETATM 3942 2H7 PC5 B 601 39.552 23.062 6.018 1.00 5.65 PC_e H
HETATM 3943 O1 PC5 B 601 41.518 22.603 5.667 1.00 5.35 PC_e O
HETATM 3944 P1 PC5 B 601 41.613 21.118 6.226 1.00 3.48 PC_e P
HETATM 3945 O9 PC5 B 601 42.730 20.985 7.195 1.00 4.42 PC_e O
HETATM 3946 O10 PC5 B 601 40.354 20.672 6.855 1.00 2.79 PC_e O
HETATM 3947 O4 PC5 B 601 41.880 20.402 4.833 1.00 4.76 PC_e O
HETATM 3948 C5 PC5 B 601 42.956 20.712 4.043 1.00 7.42 PC_e C
HETATM 3949 1H5 PC5 B 601 43.771 20.825 4.639 1.00 19.07 PC_e H
HETATM 3950 2H5 PC5 B 601 42.796 21.592 3.575 1.00 11.06 PC_e H
HETATM 3951 C4 PC5 B 601 43.221 19.673 2.975 1.00 9.96 PC_e C
HETATM 3952 1H4 PC5 B 601 43.935 20.051 2.367 1.00 22.42 PC_e H
HETATM 3953 2H4 PC5 B 601 43.636 18.887 3.457 1.00 17.33 PC_e H
HETATM 3954 N1 PC5 B 601 42.131 19.141 2.059 1.00 6.27 PC_e N
HETATM 3955 C1 PC5 B 601 41.385 20.220 1.479 1.00 15.70 PC_e C
HETATM 3956 1H1 PC5 B 601 41.229 20.521 1.396 1.00 47.92 PC_e H
HETATM 3957 2H1 PC5 B 601 41.138 20.439 1.317 1.00 48.27 PC_e H
HETATM 3958 3H1 PC5 B 601 41.246 20.471 1.297 1.00 49.00 PC_e H
HETATM 3959 C2 PC5 B 601 42.701 18.348 0.940 1.00 14.67 PC_e C
HETATM 3960 1H2 PC5 B 601 42.845 18.197 0.625 1.00 44.78 PC_e H
HETATM 3961 2H2 PC5 B 601 42.782 18.131 0.666 1.00 44.87 PC_e H
HETATM 3962 3H2 PC5 B 601 42.885 18.138 0.701 1.00 47.63 PC_e H
HETATM 3963 C3 PC5 B 601 41.245 18.285 2.806 1.00 11.94 PC_e C
HETATM 3964 1H3 PC5 B 601 41.049 18.134 3.051 1.00 45.69 PC_e H
HETATM 3965 2H3 PC5 B 601 41.090 17.992 2.979 1.00 43.73 PC_e H
HETATM 3966 3H3 PC5 B 601 40.961 18.090 2.928 1.00 41.92 PC_e H
Complement of information: that is the average structure of a 50 ns molecular dynamic
Take the closest to average but not the average as the average will have distorted geometries!
OK. Problem solved !
Thanks for your help !