Question: Adding New Atom To Parameter File In Autodock
0
gravatar for vijay
5.1 years ago by
vijay1.3k
Chennai
vijay1.3k wrote:

Dear All,

I am trying to dock my ligand acetyl coA with a receptor using autodock. When I try to run the grid, I encountered an error saying the parameters for the atom Ho were missing in the parameter file. The downloaded PDB ligand file is as below(have highlighted the atoms that are in question).

ATOM 1 N1A ACO 0 4.880 1.108 -10.650 1.00 20.00 N+0

ATOM 2 C2A ACO 0 3.865 1.949 -10.587 1.00 20.00 C+0

ATOM 3 N3A ACO 0 2.906 1.834 -9.692 1.00 20.00 N+0

ATOM 4 C4A ACO 0 2.922 0.844 -8.806 1.00 20.00 C+0

ATOM 5 C5A ACO 0 3.985 -0.074 -8.828 1.00 20.00 C+0

ATOM 6 C6A ACO 0 4.984 0.090 -9.802 1.00 20.00 C+0

ATOM 7 N6A ACO 0 6.052 -0.786 -9.876 1.00 20.00 N+0

ATOM 8 N7A ACO 0 3.765 -0.963 -7.830 1.00 20.00 N+0

ATOM 9 C8A ACO 0 2.664 -0.653 -7.208 1.00 20.00 C+0

ATOM 10 N9A ACO 0 2.109 0.457 -7.771 1.00 20.00 N+0

ATOM 11 C1B ACO 0 0.867 1.113 -7.352 1.00 20.00 C+0

ATOM 12 C2B ACO 0 -0.359 0.446 -8.025 1.00 20.00 C+0

ATOM 13 O2B ACO 0 -0.607 1.017 -9.312 1.00 20.00 O+0

ATOM 14 C3B ACO 0 -1.502 0.796 -7.036 1.00 20.00 C+0

ATOM 15 O3B ACO 0 -2.229 1.937 -7.496 1.00 20.00 O+0

ATOM 16 P3B ACO 0 -3.762 1.474 -7.665 1.00 20.00 P+0

ATOM 17 O7A ACO 0 -4.284 1.009 -6.361 1.00 20.00 O+0

ATOM 18 O8A ACO 0 -4.644 2.717 -8.184 1.00 20.00 O+0

ATOM 19 O9A ACO 0 -3.845 0.274 -8.736 1.00 20.00 O+0

ATOM 20 C4B ACO 0 -0.771 1.110 -5.716 1.00 20.00 C+0

ATOM 21 O4B ACO 0 0.633 0.905 -5.943 1.00 20.00 O+0

ATOM 22 C5B ACO 0 -1.262 0.171 -4.613 1.00 20.00 C+0

ATOM 23 O5B ACO 0 -0.574 0.464 -3.396 1.00 20.00 O+0

ATOM 24 P1A ACO 0 -1.138 -0.555 -2.285 1.00 20.00 P+0

ATOM 25 O1A ACO 0 -0.875 -1.947 -2.714 1.00 20.00 O+0

ATOM 26 O2A ACO 0 -2.724 -0.337 -2.112 1.00 20.00 O+0

ATOM 27 O3A ACO 0 -0.401 -0.279 -0.880 1.00 20.00 O+0

ATOM 28 P2A ACO 0 -1.010 -1.329 0.178 1.00 20.00 P+0

ATOM 29 O4A ACO 0 -2.470 -1.116 0.299 1.00 20.00 O+0

ATOM 30 O5A ACO 0 -0.727 -2.830 -0.330 1.00 20.00 O+0

ATOM 31 O6A ACO 0 -0.315 -1.108 1.613 1.00 20.00 O+0

ATOM 32 CBP ACO 0 -0.273 -1.907 3.893 1.00 20.00 C+0

ATOM 33 CCP ACO 0 -0.894 -2.063 2.504 1.00 20.00 C+0

ATOM 34 CDP ACO 0 -0.542 -0.494 4.416 1.00 20.00 C+0

ATOM 35 CEP ACO 0 1.236 -2.140 3.807 1.00 20.00 C+0

ATOM 36 CAP ACO 0 -0.893 -2.929 4.847 1.00 20.00 C+0

ATOM 37 OAP ACO 0 -0.744 -4.242 4.302 1.00 20.00 O+0

ATOM 38 C9P ACO 0 -0.197 -2.858 6.182 1.00 20.00 C+0

ATOM 39 O9P ACO 0 0.579 -3.730 6.508 1.00 20.00 O+0

ATOM 40 N8P ACO 0 -0.438 -1.825 7.013 1.00 20.00 N+0

ATOM 41 C7P ACO 0 0.252 -1.745 8.302 1.00 20.00 C+0

ATOM 42 C6P ACO 0 -0.197 -0.486 9.046 1.00 20.00 C+0

ATOM 43 C5P ACO 0 0.513 -0.404 10.372 1.00 20.00 C+0

ATOM 44 O5P ACO 0 1.302 -1.268 10.691 1.00 20.00 O+0

ATOM 45 N4P ACO 0 0.272 0.628 11.203 1.00 20.00 N+0

ATOM 46 C3P ACO 0 0.963 0.708 12.492 1.00 20.00 C+0

ATOM 47 C2P ACO 0 0.513 1.968 13.235 1.00 20.00 C+0

ATOM 48 S1P ACO 0 1.367 2.066 14.828 1.00 20.00 S+0

ATOM 49 C ACO 0 0.700 3.522 15.434 1.00 20.00 C+0

ATOM 50 O ACO 0 -0.111 4.137 14.775 1.00 20.00 O+0

ATOM 51 CH3 ACO 0 1.122 4.039 16.785 1.00 20.00 C+0

ATOM 52 H2A ACO 0 3.819 2.763 -11.296 1.00 20.00 H+0

ATOM 53 H61A ACO 0 6.736 -0.662 -10.553 1.00 20.00 H+0

ATOM 54 H62A ACO 0 6.117 -1.525 -9.251 1.00 20.00 H+0

ATOM 55 H8A ACO 0 2.251 -1.195 -6.371 1.00 20.00 H+0

ATOM 56 H1B ACO 0 0.900 2.177 -7.583 1.00 20.00 H+0

ATOM 57 H2B ACO 0 -0.224 -0.632 -8.099 1.00 20.00 H+0

ATOM 58 HO2A ACO 0 0.177 0.844 -9.850 1.00 20.00 H+0

ATOM 59 H3B ACO 0 -2.170 -0.054 -6.908 1.00 20.00 H+0

ATOM 60 HO8A ACO 0 -5.552 2.398 -8.272 1.00 20.00 H+0

ATOM 61 HO9A ACO 0 -3.496 0.619 -9.569 1.00 20.00 H+0

ATOM 62 H4B ACO 0 -0.952 2.146 -5.429 1.00 20.00 H+0

ATOM 63 H51A ACO 0 -1.067 -0.861 -4.901 1.00 20.00 H+0

ATOM 64 H52A ACO 0 -2.334 0.310 -4.468 1.00 20.00 H+0

ATOM 65 HO2A ACO 0 -2.851 0.579 -1.832 1.00 20.00 H+0

ATOM 66 HO5A ACO 0 0.232 -2.926 -0.395 1.00 20.00 H+0

ATOM 67 H121 ACO 0 -0.702 -3.070 2.132 1.00 20.00 H+0

ATOM 68 H122 ACO 0 -1.969 -1.897 2.565 1.00 20.00 H+0

ATOM 69 H131 ACO 0 -1.609 -0.372 4.602 1.00 20.00 H+0

ATOM 70 H132 ACO 0 0.008 -0.338 5.343 1.00 20.00 H+0

ATOM 71 H133 ACO 0 -0.217 0.235 3.674 1.00 20.00 H+0

ATOM 72 H141 ACO 0 1.427 -3.146 3.435 1.00 20.00 H+0

ATOM 73 H142 ACO 0 1.677 -1.411 3.127 1.00 20.00 H+0

ATOM 74 H143 ACO 0 1.678 -2.028 4.797 1.00 20.00 H+0

ATOM 75 H10 ACO 0 -1.953 -2.709 4.978 1.00 20.00 H+0

ATOM 76 HO1 ACO 0 0.205 -4.396 4.202 1.00 20.00 H+0

ATOM 77 HN8 ACO 0 -1.070 -1.134 6.758 1.00 20.00 H+0

ATOM 78 H71 ACO 0 1.328 -1.703 8.135 1.00 20.00 H+0

ATOM 79 H72 ACO 0 0.011 -2.625 8.899 1.00 20.00 H+0

ATOM 80 H61 ACO 0 -1.274 -0.528 9.212 1.00 20.00 H+0

ATOM 81 H62 ACO 0 0.043 0.393 8.449 1.00 20.00 H+0

ATOM 82 HN4 ACO 0 -0.358 1.319 10.947 1.00 20.00 H+0

ATOM 83 H31 ACO 0 2.040 0.750 12.325 1.00 20.00 H+0

ATOM 84 H32 ACO 0 0.722 -0.171 13.089 1.00 20.00 H+0

ATOM 85 H21 ACO 0 -0.562 1.926 13.402 1.00 20.00 H+0

ATOM 86 H22 ACO 0 0.754 2.847 12.638 1.00 20.00 H+0

ATOM 87 HH31 ACO 0 0.595 4.969 16.998 1.00 20.00 H+0

ATOM 88 HH32 ACO 0 0.879 3.300 17.549 1.00 20.00 H+0

ATOM 89 HH33 ACO 0 2.196 4.221 16.785 1.00 20.00 H+0

END

I then tried to include this atom type in the parameter file. I calculated the radii of the HO atom which is one of the parameters by adding the vanderwall radii of hydrogen and oxygen!! Please can someone let me know if this is the right approach? And how should I calculate other parameters like atomic solvation parameter, hydrogen bond radii, hydrogen bond well depth etc..

• 1.8k views
ADD COMMENTlink modified 5.1 years ago by Flow1.5k • written 5.1 years ago by vijay1.3k

Hi, you can search for atom with properties similar to HO. Then you can include the values in the similar atom to HO and add it in the parameter file. It should work fine.

ADD REPLYlink written 5.1 years ago by sris830
0
gravatar for Flow
5.1 years ago by
Flow1.5k
Flow1.5k wrote:

To which protein are you trying to dock the ligand to?

ADD COMMENTlink written 5.1 years ago by Flow1.5k
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