Error while inputting Acpype parametrized ligand into the CHARMM-GUI workflow.

User discussions
1

I have been facing issues with the platform while inputting the custom ligand topology and parameter files. I generated the top and parameter files from
the ACPYPE server (About Wonpil Im) in CHARMM
format. I wanted to use these files instead of the one’s created by CgenFF
on CHARMM-GUI.
I am stuck with the following error.

Output Excerpt from step1_pdbreader.out:

471 472 474 475 473 476 477 478 479 480

481 482 483 484 485 486 487 488 489 490

491 492 493 494 495 496 497 498 499 500

501 502 503 504 505 506 507 508 509 510

511 512 513 514 515 516 517 518 519 520

521 522 523 524 525 526 527 528 529 530

531 532 533 534 535 536 537 538 539 540

541 542 543 547 548 544 545 546 549 550

551 552 553 554 555 556 557 558 559 560

561 562 563 564 565 566 567 568 569 570

571 572 573 574 575 576 577 581 582 583

584 585 586 587 588 579 578 580 592 589

590 591 593 594 597 596 595 601 599 600

598 614 603 604 602 612 608 605 607 606

613 609 610 611 615 616 617 618 619 620

621 622 623 624 628 633 635 634 638 636

632 629 643 641 631 637 639 627 642 630

625 640 626 644 645 646 647 648 649 650

651 652 653 654 655 656 657 658 659 660

661 748 663 664 744 666 667 668 669 670

671 672 673 674 675 676 677 678 679 680

681 682 683 684 685 686 687 688 689 690

691 692 693 694 695 696 697 698 699 700

701 702 703 704 705 706 707 708 709 710

711 712 713 714 715 716 717 718 719 720

721 722 723 724 725 726 727 728 729 730

731 732 733 734 735 736 737 738

***** LEVEL -3 WARNING FROM *****
***** Null nonbond group found. Redo.

BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS 5

I was wondering if you could please help me with this error.
Your guidance is much appreciated.

Best regards,
Shubhangi

2

ACPYPE uses Antechamber and is designed for the AMBER family of force fields. For CHARMM, use CGenFF. CHARMM-GUI can automatically call CGenFF to parametrize ligands and other nonstandard species.