Dear Amber users!
I've noticed an issue related to the parametrization of the
protein-ligand complex for the system where ligand was located in the
following format:
ATOM 1 N SER A 1 -2.390 4.343 -17.003 1.00 0.00 N
ATOM 2 CA SER A 1 -2.066 5.647 -16.370 1.00 0.00 C
ATOM 3 C SER A 1 -2.394 5.608 -14.874 1.00 0.00 C
ATOM 4 O SER A 1 -3.014 4.627 -14.405 1.00 0.00 O
ATOM 5 CB SER A 1 -2.771 6.798 -17.057 1.00 0.00 C
ATOM 6 OG SER A 1 -2.538 8.023 -16.373 1.00 0.00 O
ATOM 7 H SER A 1 -1.598 3.739 -16.938 1.00 0.00 H
ATOM 8 HG SER A 1 -1.651 7.984 -15.917 1.00 0.00 H
ATOM 9 H2 SER A 1 -3.166 3.931 -16.530 1.00 0.00 H
ATOM 10 H3 SER A 1 -2.621 4.491 -17.962 1.00 0.00 H
ATOM 11 N lig 888 5.333 -3.914 24.369 1.00 0.00 N
ATOM 12 N lig 888 6.549 -3.483 22.354 1.00 0.00 N
ATOM 13 C lig 888 8.476 0.870 21.339 1.00 0.00 C
ATOM 14 C lig 888 8.480 -0.313 22.272 1.00 0.00 C
ATOM 15 C lig 888 7.515 -1.318 21.616 1.00 0.00 C
ATOM 16 C lig 888 6.759 -0.499 20.602 1.00 0.00 C
ATOM 17 C lig 888 5.725 -0.890 19.765 1.00 0.00 C
ATOM 18 C lig 888 5.391 -0.063 18.682 1.00 0.00 C
ATOM 19 C lig 888 6.087 1.136 18.438 1.00 0.00 C
ATOM 20 C lig 888 7.107 1.542 19.296 1.00 0.00 C
ATOM 21 C lig 888 7.411 0.711 20.359 1.00 0.00 C
ATOM 22 C lig 888 6.779 -2.149 22.642 1.00 0.00 C
ATOM 23 C lig 888 4.488 -6.115 24.861 1.00 0.00 C
ATOM 24 C lig 888 5.020 -6.582 23.664 1.00 0.00 C
ATOM 25 C lig 888 4.667 -4.783 25.169 1.00 0.00 C
ATOM 26 C lig 888 5.707 -5.691 22.826 1.00 0.00 C
ATOM 27 C lig 888 5.847 -4.361 23.208 1.00 0.00 C
ATOM 28 O lig 888 9.213 1.838 21.395 1.00 0.00 O
ATOM 29 O lig 888 6.362 -1.559 23.645 1.00 0.00 O
ATOM 30 CL lig 888 3.637 -7.165 25.918 1.00 0.00 Cl
ATOM 31 H lig 888 8.130 -0.030 23.243 1.00 0.00 H
ATOM 32 H lig 888 9.460 -0.720 22.413 1.00 0.00 H
ATOM 33 H lig 888 7.967 -2.125 21.077 1.00 0.00 H
ATOM 34 H lig 888 5.212 -1.769 19.935 1.00 0.00 H
ATOM 35 H lig 888 4.621 -0.338 18.052 1.00 0.00 H
ATOM 36 H lig 888 5.842 1.716 17.621 1.00 0.00 H
ATOM 37 H lig 888 7.614 2.429 19.144 1.00 0.00 H
ATOM 38 H lig 888 4.910 -7.572 23.396 1.00 0.00 H
ATOM 39 H lig 888 4.274 -4.429 26.056 1.00 0.00 H
ATOM 40 H lig 888 6.105 -6.021 21.932 1.00 0.00 H
ATOM 41 H lig 888 6.894 -3.841 21.504 1.00 0.00 H
ATOM 42 N GLY A 2 -1.982 6.655 -14.162 1.00 0.00 N
ATOM 43 CA GLY A 2 -2.172 6.779 -12.716 1.00 0.00 C
ATOM 44 C GLY A 2 -0.888 6.336 -12.067 1.00 0.00 C
ATOM 45 O GLY A 2 -0.168 5.459 -12.608 1.00 0.00 O
ATOM 46 H GLY A 2 -1.502 7.396 -14.733 1.00 0.00 H
ATOM 47 N PHE A 3 -0.636 6.866 -10.900 1.00 0.00 N
ATOM 48 CA PHE A 3 0.622 6.595 -10.191 1.00 0.00 C
ATOM 49 C PHE A 3 0.279 6.570 -8.716 1.00 0.00 C
ATOM 50 O PHE A 3 -0.265 7.544 -8.167 1.00 0.00 O
ATOM 51 CB PHE A 3 1.705 7.584 -10.641 1.00 0.00 C
ATOM 52 CG PHE A 3 3.092 7.116 -10.280 1.00 0.00 C
ATOM 53 CD1 PHE A 3 3.740 6.169 -11.037 1.00 0.00 C
ATOM 54 CD2 PHE A 3 3.702 7.569 -9.120 1.00 0.00 C
ATOM 55 CE1 PHE A 3 4.998 5.716 -10.688 1.00 0.00 C
ATOM 56 CE2 PHE A 3 4.961 7.113 -8.763 1.00 0.00 C
ATOM 57 CZ PHE A 3 5.603 6.182 -9.547 1.00 0.00 C
ATOM 58 H PHE A 3 -1.376 7.483 -10.514 1.00 0.00 H
ATOM 59 N ARG A 4 0.520 5.417 -8.096 1.00 0.00 N
ATOM 60 CA ARG A 4 0.098 5.156 -6.714 1.00 0.00 C
ATOM 61 C ARG A 4 1.298 4.777 -5.853 1.00 0.00 C
ATOM 62 O ARG A 4 2.162 4.071 -6.335 1.00 0.00 O
ATOM 63 CB ARG A 4 -0.925 4.007 -6.692 1.00 0.00 C
ATOM 64 CG ARG A 4 -2.344 4.474 -6.957 1.00 0.00 C
ATOM 65 CD ARG A 4 -2.920 5.126 -5.707 1.00 0.00 C
ATOM 66 NE ARG A 4 -4.312 5.587 -5.850 1.00 0.00 N
ATOM 67 CZ ARG A 4 -5.032 6.120 -4.869 1.00 0.00 C
ATOM 68 NH1 ARG A 4 -4.492 6.258 -3.670 1.00 0.00 N1+
ATOM 69 NH2 ARG A 4 -6.274 6.533 -5.067 1.00 0.00 N
ATOM 70 H ARG A 4 1.033 4.714 -8.673 1.00 0.00 H
ATOM 71 HE ARG A 4 -4.742 5.489 -6.755 1.00 0.00 H
ATOM 72 HH11 ARG A 4 -3.553 5.993 -3.480 1.00 0.00 H
ATOM 73 HH12 ARG A 4 -5.049 6.647 -2.917 1.00 0.00 H
ATOM 74 HH21 ARG A 4 -6.665 6.453 -5.994 1.00 0.00 H
ATOM 75 HH22 ARG A 4 -6.810 6.913 -4.326 1.00 0.00 H
In that case tleap considered the first Ser residue as the separate
part from the rest of the protein
When I modified pdb replacing the lig residue before the protein atoms
everything was OK. Could you suggest an automatic way to resolve such
issue?
Many thanks in advance
Enricro
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Received on Thu Aug 04 2022 - 13:36:50 PDT
