[gmx-users] producing top and gro files for the molecule with metal ions.
Anna Reymer
anna.reymer at gmail.com
Tue Jun 26 17:13:06 CEST 2007
Hi!
I am running GROMACS for DNA with Ruthenium (II) complex. Please have
a look into pdb file below.
There is no parameters for any of transitional metals to produce
topology and coordinates for it. The Dundee PRODRG server
(http://davapc1.bioch.dundee.ac.uk/programs/prodrg/ ) has parameters
only for C, N, O, S, P, H, F, Cl, Br, I the same situation is with
ANTECHAMBER (http://amber.scripps.edu/antechamber/antechamber.html).
Is it possible somehow to produce topology and coordinates files ?
I will appreciate any help!
regards
HETATM 1 C 1 95.427 15.980 -11.287
HETATM 2 C 2 96.704 16.174 -11.867
HETATM 3 C 3 96.881 16.022 -13.249
HETATM 4 C 4 95.808 15.620 -14.056
HETATM 5 C 5 94.537 15.427 -13.486
HETATM 6 C 6 94.336 15.629 -12.113
HETATM 7 N 7 95.980 15.457 -15.378
HETATM 8 N 8 93.498 15.082 -14.263
HETATM 9 Ru 9 92.469 13.729 -20.372
HETATM 10 C 10 93.677 14.881 -15.584
HETATM 11 C 11 94.947 15.071 -16.155
HETATM 12 C 12 95.118 14.876 -17.537
HETATM 13 C 13 92.598 14.508 -16.408
HETATM 14 C 14 94.031 14.467 -18.364
HETATM 15 C 15 92.780 14.285 -17.804
HETATM 16 C 16 96.385 15.084 -18.114
HETATM 17 C 17 96.549 14.888 -19.486
HETATM 18 C 18 95.436 14.502 -20.233
HETATM 19 N 19 94.215 14.277 -19.708
HETATM 20 N 20 91.722 13.918 -18.593
HETATM 21 C 21 91.317 14.347 -15.844
HETATM 22 C 22 90.254 13.974 -16.667
HETATM 23 C 23 90.513 13.751 -18.019
HETATM 24 C 24 89.450 9.684 -21.011
HETATM 25 C 25 90.546 9.017 -20.462
HETATM 26 C 26 91.702 9.738 -20.134
HETATM 27 C 27 92.794 9.044 -19.588
HETATM 28 C 28 93.942 9.757 -19.242
HETATM 29 C 29 93.939 11.141 -19.444
HETATM 30 N 30 92.908 11.833 -19.972
HETATM 31 C 31 91.771 11.152 -20.325
HETATM 32 C 32 90.680 11.817 -20.863
HETATM 33 C 33 89.516 11.070 -21.220
HETATM 34 N 34 90.705 13.176 -21.050
HETATM 35 C 35 88.401 11.722 -21.774
HETATM 36 C 36 88.456 13.103 -21.975
HETATM 37 C 37 89.624 13.772 -21.593
HETATM 38 C 38 93.459 16.301 -24.653
HETATM 39 C 39 92.867 17.340 -23.935
HETATM 40 C 40 92.378 17.098 -22.644
HETATM 41 C 41 91.773 18.155 -21.943
HETATM 42 C 42 91.292 17.920 -20.654
HETATM 43 C 43 91.464 16.643 -20.110
HETATM 44 N 44 92.035 15.609 -20.763
HETATM 45 C 45 92.499 15.812 -22.037
HETATM 46 C 46 93.090 14.781 -22.748
HETATM 47 C 47 93.563 15.028 -24.072
HETATM 48 N 48 93.227 13.534 -22.192
HETATM 49 C 49 94.161 13.993 -24.812
HETATM 50 C 50 94.272 12.726 -24.233
HETATM 51 C 51 93.795 12.559 -22.929
HETATM 52 C 52 93.954 16.227 -9.310
HETATM 53 C 53 95.244 16.108 -9.878
HETATM 54 C 54 96.370 16.082 -9.032
HETATM 55 C 55 96.209 16.124 -7.645
HETATM 56 C 56 94.932 16.253 -7.076
HETATM 57 C 57 93.810 16.331 -7.915
HETATM 58 N 58 97.295 16.071 -6.858
HETATM 59 N 59 94.799 16.334 -5.742
HETATM 60 Ru 60 98.592 16.096 -0.641
HETATM 61 C 61 95.886 16.246 -4.946
HETATM 62 C 62 97.162 16.109 -5.519
HETATM 63 C 63 98.298 16.036 -4.692
HETATM 64 C 64 95.764 16.320 -3.547
HETATM 65 C 65 98.167 16.076 -3.271
HETATM 66 C 66 96.912 16.220 -2.704
HETATM 67 C 67 99.581 15.917 -5.271
HETATM 68 C 68 100.695 15.814 -4.436
HETATM 69 C 69 100.484 15.852 -3.056
HETATM 70 N 70 99.278 15.989 -2.472
HETATM 71 N 71 96.775 16.294 -1.343
HETATM 72 C 72 94.488 16.491 -2.970
HETATM 73 C 73 94.375 16.574 -1.581
HETATM 74 C 74 95.543 16.468 -0.823
HETATM 75 C 75 97.470 19.389 3.075
HETATM 76 C 76 97.923 20.308 2.129
HETATM 77 C 77 98.376 19.853 0.883
HETATM 78 C 78 98.823 20.799 -0.057
HETATM 79 C 79 99.266 20.354 -1.304
HETATM 80 C 80 99.235 18.979 -1.556
HETATM 81 N 81 98.816 18.048 -0.673
HETATM 82 C 82 98.375 18.462 0.558
HETATM 83 C 83 97.921 17.549 1.497
HETATM 84 C 84 97.470 18.020 2.767
HETATM 85 N 85 97.896 16.206 1.219
HETATM 86 C 86 97.011 17.111 3.737
HETATM 87 C 87 97.009 15.747 3.437
HETATM 88 C 88 97.458 15.357 2.171
HETATM 89 C 89 101.850 12.641 1.177
HETATM 90 C 90 100.792 11.783 0.884
HETATM 91 C 91 99.646 12.286 0.254
HETATM 92 C 92 98.615 11.392 -0.079
HETATM 93 C 93 97.493 11.877 -0.752
HETATM 94 C 94 97.411 13.255 -0.970
HETATM 95 N 95 98.361 14.144 -0.611
HETATM 96 C 96 99.508 13.680 -0.022
HETATM 97 C 97 100.538 14.544 0.316
HETATM 98 C 98 101.730 14.010 0.894
HETATM 99 N 99 100.434 15.893 0.084
HETATM 100 C 100 102.818 14.853 1.174
HETATM 101 C 101 102.697 16.221 0.918
HETATM 102 C 102 101.485 16.680 0.390
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