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    problem of exporting the atomic model of DNA to PDB

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      Dominic last edited by

      When exporting an atomic DNA model to PDB for use in other programs (e.g., Schrodinger Suite), ATOM records are marked as HETATM, and residues have the non-standard name N A, which causes import problems. How can I correctly export a full-atom PDB that is compatible with standard molecular software?b5d507cd-6e9f-4153-b1df-75a0e1af912a-image.png Example: AUTHOR GENERATED BY SAMSON 2025 R2 (8.0.0)
      MODEL 1
      HETATM 1 P N A 148.476-407.921 -26.809 0.00 P
      HETATM 2 OP1 N A 148.722-409.286 -26.289 0.00 O
      HETATM 3 OP2 N A 149.239-406.836 -26.153 0.00 O
      HETATM 4 O5' N A 148,735-407,888 -28,387 0.00 O
      HETATM 5 C5' N A 147,743-408,444 -29,270 0.00 C
      HETATM 6 C4' N A 148,403-408,954 -30,537 0.00 C
      HETATM 7 O4' N A 148,519-407,853 -31,484 0.00 O
      HETATM 8 C3' N A 149,833-409,471 -30,379 0.00 C
      HETATM 9 O3' N A 150,178-410,357 -31,440 0.00 O
      HETATM 10 C2' N A 150,670-408,202 -30,528 0.00 C
      HETATM 11 C1' N A 149,866-407,411 -31,556 0.00 C
      HETATM 12 N9 N A 149,881-405,940 -31,325 0.00 N
      HETATM 13 C8 N A 149,897-405,249 -30,135 0.00 C
      HETATM 14 N7 N A 149,908-403,959 -30,275 0.00 N
      HETATM 15 C5 N A 149,897-403,771 -31,650 0.00 C
      HETATM 16 C6 N A 149,899-402,616 -32,448 0.00 C
      HETATM 17 N6 N A 149,915-401,372 -31,948 0.00 N
      HETATM 18 N1 N A 149,885-402,785 -33,783 0.00 N
      HETATM 19 C2 N A 149,870-404,023 -34,273 0.00 C
      CONECT 444 442
      CONECT 445 442 446
      CONECT 446 445 447
      CONECT 447 446 448 449
      CONECT 448 447 452
      CONECT 449 447 450 451
      CONECT 450 449
      CONECT 451 449 452
      CONECT 452 448 451 453
      CONECT 453 452 454 462
      CONECT 454 453 455
      CONECT 455 454 456
      CONECT 456 455 457 462
      CONECT 457 456 458 459
      CONECT 458 457
      CONECT 459 457 460
      CONECT 460 459 461
      CONECT 461 460 462
      CONECT 462 453 456 461
      MASTER 0 0 0 0 0 0 0 0 473 2 462 0
      END

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