Hi,
The PDB you posted does not conform to the standard. You've got a
ligand with no chain ID inserted into the middle of your protein chain
A (and not a TER card in sight). As you discovered, there's no way to
automatically resolve this past moving the ligand either to the
beginning or the end and separating the chains with TER cards. I'm not
sure how you obtained the original PDB but in my opinion the real
solution would be to fix that so it produces "better" PDBs.
-Dan
On Mon, Jul 25, 2022 at 4:44 AM Enrico Martinez via AMBER
<amber.ambermd.org> wrote:
>
> 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 Mon Aug 08 2022 - 07:30:05 PDT
