Pdb2gmx residues in the chain do not have consistent type. Simulated protein contains D-amino acids

User discussions
1

GROMACS version: version 2024.1
GROMACS modification: No

I’m running into a problem where pdb2gmx does not recognize D-amino acids named with the DXXX (XXX = 3 letter code) convention as having type=ATOM, even though it is named as such in the input pdb file. I suspect this has something to do with the spacing of the resn column and chain column in my input pdb file. For the D-residues the resn runs into the chain ID column with no space.

Here is my input command:
gmx pdb2gmx -f 2GB1_Rip_R_0131w.pdb -ff charmm36_ljpme-jul2022 -o 2GB1_131.gro -ignh -ter

Here is the output from pdb2gmx:
[samdintd@cn0053 output_S4_1_0131]$ gmx pdb2gmx -f 2GB1_Rip_R_0131w.pdb -ff charmm36_ljpme-jul2022 -o 2GB1_131.gro -ignh -v -merge interactive -ter
:-) GROMACS - gmx pdb2gmx, 2024.1 (-:

Executable: /usr/local/apps/gromacs/2024.1-intel2024.0/bin/gmx
Data prefix: /usr/local/apps/gromacs/2024.1-intel2024.0
Working dir: /gpfs/gsfs12/users/samdintd/gromacs/Ripple/strand_4/output_S4_1_0131
Command line:
gmx pdb2gmx -f 2GB1_Rip_R_0131w.pdb -ff charmm36_ljpme-jul2022 -o 2GB1_131.gro -ignh -v -merge interactive -ter

Using the Charmm36_ljpme-jul2022 force field in directory ./charmm36_ljpme-jul2022.ff
Opening force field file ./charmm36_ljpme-jul2022.ff/watermodels.dat

Select the Water Model:

1: TIP3P CHARMM-modified TIP3P water model (recommended over original TIP3P)

2: TIP3P_ORIGINAL Original TIP3P water model

3: SPC SPC water model

4: SPCE SPC/E water model

5: TIP5P TIP5P water model

6: TIP4P TIP4P water model

7: TIP4PEW TIP4P/Ew water model

8: None
1

going to rename ./charmm36_ljpme-jul2022.ff/aminoacids.r2b
Opening force field file ./charmm36_ljpme-jul2022.ff/aminoacids.r2b

going to rename ./charmm36_ljpme-jul2022.ff/carb.r2b
Opening force field file ./charmm36_ljpme-jul2022.ff/carb.r2b

going to rename ./charmm36_ljpme-jul2022.ff/cgenff.r2b
Opening force field file ./charmm36_ljpme-jul2022.ff/cgenff.r2b

going to rename ./charmm36_ljpme-jul2022.ff/ethers.r2b
Opening force field file ./charmm36_ljpme-jul2022.ff/ethers.r2b

going to rename ./charmm36_ljpme-jul2022.ff/lipid.r2b
Opening force field file ./charmm36_ljpme-jul2022.ff/lipid.r2b

going to rename ./charmm36_ljpme-jul2022.ff/metals.r2b
Opening force field file ./charmm36_ljpme-jul2022.ff/metals.r2b

going to rename ./charmm36_ljpme-jul2022.ff/na.r2b
Opening force field file ./charmm36_ljpme-jul2022.ff/na.r2b

going to rename ./charmm36_ljpme-jul2022.ff/silicates.r2b
Opening force field file ./charmm36_ljpme-jul2022.ff/silicates.r2b

going to rename ./charmm36_ljpme-jul2022.ff/solvent.r2b
Opening force field file ./charmm36_ljpme-jul2022.ff/solvent.r2b
Reading 2GB1_Rip_R_0131w.pdb…
WARNING: all CONECT records are ignored
Read ‘’, 442 atoms
Renaming atom ‘CD1’ in residue 6 ILE to ‘CD’
Renaming atom ‘CD1’ in residue 27 ILE to ‘CD’

Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.

There are 1 chains and 0 blocks of water and 56 residues with 442 atoms

chain #res #atoms

1 ‘A’ 56 442

All occupancies are one
All occupancies are one
Opening force field file ./charmm36_ljpme-jul2022.ff/atomtypes.atp

Reading residue database… (Charmm36_ljpme-jul2022)
Opening force field file ./charmm36_ljpme-jul2022.ff/aminoacids.rtp
Opening force field file ./charmm36_ljpme-jul2022.ff/carb.rtp
Opening force field file ./charmm36_ljpme-jul2022.ff/cgenff.rtp
Opening force field file ./charmm36_ljpme-jul2022.ff/ethers.rtp
Opening force field file ./charmm36_ljpme-jul2022.ff/lipid.rtp
Opening force field file ./charmm36_ljpme-jul2022.ff/metals.rtp
Opening force field file ./charmm36_ljpme-jul2022.ff/na.rtp
Opening force field file ./charmm36_ljpme-jul2022.ff/silicates.rtp
Opening force field file ./charmm36_ljpme-jul2022.ff/solvent.rtp
Opening force field file ./charmm36_ljpme-jul2022.ff/aminoacids.hdb
Opening force field file ./charmm36_ljpme-jul2022.ff/carb.hdb
Opening force field file ./charmm36_ljpme-jul2022.ff/cgenff.hdb
Opening force field file ./charmm36_ljpme-jul2022.ff/ethers.hdb
Opening force field file ./charmm36_ljpme-jul2022.ff/lipid.hdb
Opening force field file ./charmm36_ljpme-jul2022.ff/metals.hdb
Opening force field file ./charmm36_ljpme-jul2022.ff/na.hdb
Opening force field file ./charmm36_ljpme-jul2022.ff/silicates.hdb
Opening force field file ./charmm36_ljpme-jul2022.ff/solvent.hdb
Opening force field file ./charmm36_ljpme-jul2022.ff/aminoacids.n.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/carb.n.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/cgenff.n.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/ethers.n.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/lipid.n.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/metals.n.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/na.n.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/silicates.n.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/solvent.n.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/aminoacids.c.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/carb.c.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/cgenff.c.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/ethers.c.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/lipid.c.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/metals.c.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/na.c.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/silicates.c.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/solvent.c.tdb

Back Off! I just backed up topol.top to ./#topol.top.9#

Processing chain 1 ‘A’ (442 atoms, 56 residues)

Program: gmx pdb2gmx, version 2024.1
Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 1042)

Fatal error:
The residues in the chain LEU1–DASN56 do not have a consistent type. The
first residue has type ‘Protein’, while residue DPHE51 is of type ‘Other’.
Either there is a mistake in your chain, or it includes nonstandard residue
names that have not yet been added to the residuetypes.dat file in the GROMACS
library directory. If there are other molecules such as ligands, they should
not have the same chain ID as the adjacent protein chain since it’s a separate
molecule.

For more information and tips for troubleshooting, please check the GROMACS
website at Common errors when using GROMACS - GROMACS 2024.4 documentation

Here is a section of my pdb file (D-residues from 51-56)

ATOM 632 N SER A 40 5.735 11.906 -5.851 1.00 0.00 A N
ATOM 633 CA SER A 40 4.603 12.222 -6.731 1.00 0.00 A C
ATOM 634 C SER A 40 4.782 11.845 -8.206 1.00 0.00 A C
ATOM 635 O SER A 40 5.519 12.512 -8.932 1.00 0.00 A O
ATOM 636 CB SER A 40 4.312 13.707 -6.641 1.00 0.00 A C
ATOM 637 OG SER A 40 3.242 14.061 -7.475 1.00 0.00 A O
ATOM 638 H SER A 40 6.660 11.742 -6.230 1.00 0.00 A H
ATOM 639 HA SER A 40 3.729 11.677 -6.371 1.00 0.00 A H
ATOM 640 1HB SER A 40 4.074 13.969 -5.610 1.00 0.00 A H
ATOM 641 2HB SER A 40 5.200 14.270 -6.925 1.00 0.00 A H
ATOM 642 HG SER A 40 3.167 13.355 -8.122 1.00 0.00 A H
ATOM 643 N GLY A 41 4.112 10.779 -8.644 1.00 0.00 A N
ATOM 644 CA GLY A 41 4.317 10.243 -9.990 1.00 0.00 A C
ATOM 645 C GLY A 41 3.035 9.516 -10.464 1.00 0.00 A C
ATOM 646 O GLY A 41 1.943 10.082 -10.419 1.00 0.00 A O
ATOM 647 H GLY A 41 3.446 10.330 -8.032 1.00 0.00 A H
ATOM 648 1HA GLY A 41 4.568 11.056 -10.671 1.00 0.00 A H
ATOM 649 2HA GLY A 41 5.164 9.557 -9.984 1.00 0.00 A H
ATOM 650 N ASN A 42 3.181 8.268 -10.913 1.00 0.00 A N
ATOM 651 CA ASN A 42 2.115 7.432 -11.474 1.00 0.00 A C
ATOM 652 C ASN A 42 1.279 6.649 -10.448 1.00 0.00 A C
ATOM 653 O ASN A 42 1.708 5.643 -9.874 1.00 0.00 A O
ATOM 654 CB ASN A 42 2.714 6.470 -12.484 1.00 0.00 A C
ATOM 655 CG ASN A 42 3.263 7.171 -13.695 1.00 0.00 A C
ATOM 656 ND2 ASN A 42 4.482 6.855 -14.051 1.00 0.00 A N
ATOM 657 OD1 ASN A 42 2.581 7.999 -14.310 1.00 0.00 A O
ATOM 658 H ASN A 42 4.102 7.864 -10.856 1.00 0.00 A H
ATOM 659 HA ASN A 42 1.443 8.084 -12.030 1.00 0.00 A H
ATOM 660 1HB ASN A 42 3.517 5.901 -12.013 1.00 0.00 A H
ATOM 661 2HB ASN A 42 1.953 5.758 -12.804 1.00 0.00 A H
ATOM 662 1HD2 ASN A 42 4.898 7.289 -14.850 1.00 0.00 A H
ATOM 663 2HD2 ASN A 42 4.996 6.179 -13.524 1.00 0.00 A H
ATOM 664 N VAL A 43 0.057 7.148 -10.253 1.00 0.00 A N
ATOM 665 CA VAL A 43 -0.921 6.674 -9.274 1.00 0.00 A C
ATOM 666 C VAL A 43 -1.822 5.597 -9.892 1.00 0.00 A C
ATOM 667 O VAL A 43 -2.502 5.856 -10.885 1.00 0.00 A O
ATOM 668 CB VAL A 43 -1.786 7.845 -8.769 1.00 0.00 A C
ATOM 669 CG1 VAL A 43 -2.841 7.345 -7.793 1.00 0.00 A C
ATOM 670 CG2 VAL A 43 -0.903 8.897 -8.116 1.00 0.00 A C
ATOM 671 H VAL A 43 -0.212 7.926 -10.838 1.00 0.00 A H
ATOM 672 HA VAL A 43 -0.406 6.256 -8.409 1.00 0.00 A H
ATOM 673 HB VAL A 43 -2.313 8.286 -9.615 1.00 0.00 A H
ATOM 674 1HG1 VAL A 43 -3.443 8.185 -7.447 1.00 0.00 A H
ATOM 675 2HG1 VAL A 43 -3.484 6.620 -8.292 1.00 0.00 A H
ATOM 676 3HG1 VAL A 43 -2.353 6.873 -6.940 1.00 0.00 A H
ATOM 677 1HG2 VAL A 43 -1.521 9.722 -7.762 1.00 0.00 A H
ATOM 678 2HG2 VAL A 43 -0.371 8.454 -7.274 1.00 0.00 A H
ATOM 679 3HG2 VAL A 43 -0.182 9.270 -8.844 1.00 0.00 A H
ATOM 680 N LYS A 44 -1.823 4.394 -9.302 1.00 0.00 A N
ATOM 681 CA LYS A 44 -2.581 3.259 -9.843 1.00 0.00 A C
ATOM 682 C LYS A 44 -3.577 2.605 -8.867 1.00 0.00 A C
ATOM 683 O LYS A 44 -3.498 2.797 -7.659 1.00 0.00 A O
ATOM 684 CB LYS A 44 -1.603 2.197 -10.349 1.00 0.00 A C
ATOM 685 CG LYS A 44 -0.734 2.647 -11.516 1.00 0.00 A C
ATOM 686 CD LYS A 44 0.175 1.524 -11.993 1.00 0.00 A C
ATOM 687 CE LYS A 44 1.046 1.973 -13.157 1.00 0.00 A C
ATOM 688 NZ LYS A 44 1.939 0.883 -13.636 1.00 0.00 A N
ATOM 689 H LYS A 44 -1.278 4.270 -8.462 1.00 0.00 A H
ATOM 690 HA LYS A 44 -3.139 3.614 -10.707 1.00 0.00 A H
ATOM 691 1HB LYS A 44 -0.941 1.896 -9.536 1.00 0.00 A H
ATOM 692 2HB LYS A 44 -2.157 1.313 -10.665 1.00 0.00 A H
ATOM 693 1HG LYS A 44 -1.371 2.963 -12.343 1.00 0.00 A H
ATOM 694 2HG LYS A 44 -0.121 3.494 -11.208 1.00 0.00 A H
ATOM 695 1HD LYS A 44 0.818 1.203 -11.172 1.00 0.00 A H
ATOM 696 2HD LYS A 44 -0.430 0.676 -12.311 1.00 0.00 A H
ATOM 697 1HE LYS A 44 0.412 2.295 -13.982 1.00 0.00 A H
ATOM 698 2HE LYS A 44 1.659 2.819 -12.848 1.00 0.00 A H
ATOM 699 1HZ LYS A 44 2.499 1.221 -14.407 1.00 0.00 A H
ATOM 700 2HZ LYS A 44 2.546 0.589 -12.883 1.00 0.00 A H
ATOM 701 3HZ LYS A 44 1.381 0.100 -13.944 1.00 0.00 A H
ATOM 702 N GLN A 45 -4.523 1.825 -9.414 1.00 0.00 A N
ATOM 703 CA GLN A 45 -5.459 1.036 -8.599 1.00 0.00 A C
ATOM 704 C GLN A 45 -5.834 -0.297 -9.188 1.00 0.00 A C
ATOM 705 O GLN A 45 -6.239 -0.412 -10.345 1.00 0.00 A O
ATOM 706 CB GLN A 45 -6.740 1.838 -8.350 1.00 0.00 A C
ATOM 707 CG GLN A 45 -7.744 1.141 -7.448 1.00 0.00 A C
ATOM 708 CD GLN A 45 -8.970 1.994 -7.180 1.00 0.00 A C
ATOM 709 NE2 GLN A 45 -10.042 1.359 -6.720 1.00 0.00 A N
ATOM 710 OE1 GLN A 45 -8.954 3.211 -7.384 1.00 0.00 A O
ATOM 711 H GLN A 45 -4.592 1.781 -10.421 1.00 0.00 A H
ATOM 712 HA GLN A 45 -4.993 0.862 -7.630 1.00 0.00 A H
ATOM 713 1HB GLN A 45 -6.487 2.796 -7.897 1.00 0.00 A H
ATOM 714 2HB GLN A 45 -7.230 2.045 -9.301 1.00 0.00 A H
ATOM 715 1HG GLN A 45 -8.068 0.217 -7.926 1.00 0.00 A H
ATOM 716 2HG GLN A 45 -7.267 0.920 -6.493 1.00 0.00 A H
ATOM 717 1HE2 GLN A 45 -10.881 1.869 -6.525 1.00 0.00 A H
ATOM 718 2HE2 GLN A 45 -10.012 0.371 -6.568 1.00 0.00 A H
ATOM 719 N ASN A 46 -5.683 -1.312 -8.337 1.00 0.00 A N
ATOM 720 CA ASN A 46 -6.054 -2.661 -8.634 1.00 0.00 A C
ATOM 721 C ASN A 46 -7.391 -3.004 -8.004 1.00 0.00 A C
ATOM 722 O ASN A 46 -7.477 -3.194 -6.787 1.00 0.00 A O
ATOM 723 CB ASN A 46 -4.972 -3.620 -8.173 1.00 0.00 A C
ATOM 724 CG ASN A 46 -5.273 -5.048 -8.537 1.00 0.00 A C
ATOM 725 ND2 ASN A 46 -4.328 -5.922 -8.299 1.00 0.00 A N
ATOM 726 OD1 ASN A 46 -6.361 -5.359 -9.034 1.00 0.00 A O
ATOM 727 H ASN A 46 -5.290 -1.124 -7.444 1.00 0.00 A H
ATOM 728 HA ASN A 46 -6.121 -2.779 -9.716 1.00 0.00 A H
ATOM 729 1HB ASN A 46 -4.019 -3.336 -8.620 1.00 0.00 A H
ATOM 730 2HB ASN A 46 -4.861 -3.550 -7.091 1.00 0.00 A H
ATOM 731 1HD2 ASN A 46 -4.472 -6.887 -8.521 1.00 0.00 A H
ATOM 732 2HD2 ASN A 46 -3.463 -5.626 -7.895 1.00 0.00 A H
ATOM 733 N PRO A 47 -8.421 -3.115 -8.828 1.00 0.00 A N
ATOM 734 CA PRO A 47 -9.771 -3.362 -8.336 1.00 0.00 A C
ATOM 735 C PRO A 47 -9.941 -4.781 -7.808 1.00 0.00 A C
ATOM 736 O PRO A 47 -10.895 -5.073 -7.088 1.00 0.00 A O
ATOM 737 CB PRO A 47 -10.632 -3.120 -9.580 1.00 0.00 A C
ATOM 738 CG PRO A 47 -9.718 -3.410 -10.721 1.00 0.00 A C
ATOM 739 CD PRO A 47 -8.368 -2.937 -10.249 1.00 0.00 A C
ATOM 740 HA PRO A 47 -9.965 -2.672 -7.517 1.00 0.00 A H
ATOM 741 1HB PRO A 47 -11.513 -3.778 -9.561 1.00 0.00 A H
ATOM 742 2HB PRO A 47 -11.004 -2.084 -9.584 1.00 0.00 A H
ATOM 743 1HG PRO A 47 -9.732 -4.485 -10.954 1.00 0.00 A H
ATOM 744 2HG PRO A 47 -10.059 -2.884 -11.624 1.00 0.00 A H
ATOM 745 1HD PRO A 47 -7.583 -3.565 -10.694 1.00 0.00 A H
ATOM 746 2HD PRO A 47 -8.229 -1.883 -10.531 1.00 0.00 A H
ATOM 747 N SER A 48 -9.022 -5.664 -8.184 1.00 0.00 A N
ATOM 748 CA SER A 48 -9.076 -7.058 -7.785 1.00 0.00 A C
ATOM 749 C SER A 48 -8.401 -7.316 -6.439 1.00 0.00 A C
ATOM 750 O SER A 48 -8.447 -8.441 -5.937 1.00 0.00 A O
ATOM 751 CB SER A 48 -8.425 -7.915 -8.853 1.00 0.00 A C
ATOM 752 OG SER A 48 -7.030 -7.792 -8.815 1.00 0.00 A O
ATOM 753 H SER A 48 -8.261 -5.355 -8.773 1.00 0.00 A H
ATOM 754 HA SER A 48 -10.122 -7.348 -7.682 1.00 0.00 A H
ATOM 755 1HB SER A 48 -8.706 -8.957 -8.703 1.00 0.00 A H
ATOM 756 2HB SER A 48 -8.792 -7.615 -9.834 1.00 0.00 A H
ATOM 757 HG SER A 48 -6.841 -6.864 -8.969 1.00 0.00 A H
ATOM 758 N ARG A 49 -7.788 -6.287 -5.844 1.00 0.00 A N
ATOM 759 CA ARG A 49 -7.182 -6.450 -4.525 1.00 0.00 A C
ATOM 760 C ARG A 49 -7.603 -5.338 -3.573 1.00 0.00 A C
ATOM 761 O ARG A 49 -7.545 -5.508 -2.355 1.00 0.00 A O
ATOM 762 CB ARG A 49 -5.664 -6.469 -4.634 1.00 0.00 A C
ATOM 763 CG ARG A 49 -5.093 -7.646 -5.408 1.00 0.00 A C
ATOM 764 CD ARG A 49 -5.275 -8.925 -4.677 1.00 0.00 A C
ATOM 765 NE ARG A 49 -4.721 -10.052 -5.409 1.00 0.00 A N
ATOM 766 CZ ARG A 49 -5.397 -10.782 -6.317 1.00 0.00 A C
ATOM 767 NH1 ARG A 49 -6.649 -10.491 -6.593 1.00 0.00 A N
ATOM 768 NH2 ARG A 49 -4.803 -11.790 -6.930 1.00 0.00 A N
ATOM 769 H ARG A 49 -7.759 -5.378 -6.290 1.00 0.00 A H
ATOM 770 HA ARG A 49 -7.521 -7.393 -4.100 1.00 0.00 A H
ATOM 771 1HB ARG A 49 -5.324 -5.556 -5.122 1.00 0.00 A H
ATOM 772 2HB ARG A 49 -5.228 -6.488 -3.635 1.00 0.00 A H
ATOM 773 1HG ARG A 49 -5.597 -7.727 -6.372 1.00 0.00 A H
ATOM 774 2HG ARG A 49 -4.025 -7.492 -5.569 1.00 0.00 A H
ATOM 775 1HD ARG A 49 -4.774 -8.866 -3.711 1.00 0.00 A H
ATOM 776 2HD ARG A 49 -6.338 -9.108 -4.523 1.00 0.00 A H
ATOM 777 HE ARG A 49 -3.759 -10.307 -5.223 1.00 0.00 A H
ATOM 778 1HH1 ARG A 49 -7.104 -9.721 -6.124 1.00 0.00 A H
ATOM 779 2HH1 ARG A 49 -7.157 -11.038 -7.273 1.00 0.00 A H
ATOM 780 1HH2 ARG A 49 -3.840 -12.014 -6.718 1.00 0.00 A H
ATOM 781 2HH2 ARG A 49 -5.310 -12.337 -7.611 1.00 0.00 A H
ATOM 782 N GLY A 50 -8.016 -4.199 -4.122 1.00 0.00 A N
ATOM 783 CA GLY A 50 -8.373 -3.056 -3.294 1.00 0.00 A C
ATOM 784 C GLY A 50 -7.165 -2.223 -2.880 1.00 0.00 A C
ATOM 785 O GLY A 50 -7.011 -1.917 -1.691 1.00 0.00 A O
ATOM 786 H GLY A 50 -8.055 -4.108 -5.127 1.00 0.00 A H
ATOM 787 1HA GLY A 50 -9.072 -2.424 -3.843 1.00 0.00 A H
ATOM 788 2HA GLY A 50 -8.896 -3.403 -2.404 1.00 0.00 A H
ATOM 789 N DPHEA 51 -6.334 -1.841 -3.860 1.00 0.00 A N
ATOM 790 CA DPHEA 51 -5.165 -1.020 -3.543 1.00 0.00 A C
ATOM 791 C DPHEA 51 -4.285 -0.813 -4.725 1.00 0.00 A C
ATOM 792 O DPHEA 51 -4.666 -1.120 -5.836 1.00 0.00 A O
ATOM 793 CB DPHEA 51 -5.448 0.350 -2.879 1.00 0.00 A C
ATOM 794 CG DPHEA 51 -6.279 1.381 -3.540 1.00 0.00 A C
ATOM 795 CD1 DPHEA 51 -5.717 2.308 -4.424 1.00 0.00 A C
ATOM 796 CD2 DPHEA 51 -7.586 1.514 -3.196 1.00 0.00 A C
ATOM 797 CE1 DPHEA 51 -6.486 3.333 -4.945 1.00 0.00 A C
ATOM 798 CE2 DPHEA 51 -8.358 2.516 -3.699 1.00 0.00 A C
ATOM 799 CZ DPHEA 51 -7.816 3.438 -4.577 1.00 0.00 A C
ATOM 800 H DPHEA 51 -6.488 -2.196 -4.805 1.00 0.00 A H
ATOM 801 HA DPHEA 51 -4.584 -1.574 -2.805 1.00 0.00 A H
ATOM 802 1HB DPHEA 51 -4.496 0.827 -2.718 1.00 0.00 A H
ATOM 803 2HB DPHEA 51 -5.857 0.191 -1.891 1.00 0.00 A H
ATOM 804 HD1 DPHEA 51 -4.664 2.224 -4.688 1.00 0.00 A H
ATOM 805 HD2 DPHEA 51 -7.996 0.816 -2.511 1.00 0.00 A H
ATOM 806 HE1 DPHEA 51 -6.046 4.055 -5.632 1.00 0.00 A H
ATOM 807 HE2 DPHEA 51 -9.388 2.581 -3.401 1.00 0.00 A H
ATOM 808 HZ DPHEA 51 -8.432 4.236 -4.973 1.00 0.00 A H
ATOM 809 N DGLUA 52 -3.097 -0.290 -4.494 1.00 0.00 A N
ATOM 810 CA DGLUA 52 -2.275 0.068 -5.630 1.00 0.00 A C
ATOM 811 C DGLUA 52 -1.268 1.116 -5.214 1.00 0.00 A C
ATOM 812 O DGLUA 52 -0.536 0.947 -4.246 1.00 0.00 A O
ATOM 813 CB DGLUA 52 -1.582 -1.153 -6.231 1.00 0.00 A C
ATOM 814 CG DGLUA 52 -0.900 -0.867 -7.560 1.00 0.00 A C
ATOM 815 CD DGLUA 52 -0.315 -2.094 -8.195 1.00 0.00 A C
ATOM 816 OE1 DGLUA 52 -0.377 -3.142 -7.589 1.00 0.00 A O
ATOM 817 OE2 DGLUA 52 0.188 -1.990 -9.290 1.00 0.00 A O
ATOM 818 H DGLUA 52 -2.794 -0.154 -3.533 1.00 0.00 A H
ATOM 819 HA DGLUA 52 -2.914 0.503 -6.399 1.00 0.00 A H
ATOM 820 1HB DGLUA 52 -2.297 -1.958 -6.378 1.00 0.00 A H
ATOM 821 2HB DGLUA 52 -0.820 -1.515 -5.538 1.00 0.00 A H
ATOM 822 1HG DGLUA 52 -0.120 -0.131 -7.410 1.00 0.00 A H
ATOM 823 2HG DGLUA 52 -1.636 -0.432 -8.237 1.00 0.00 A H
ATOM 824 N DILEA 53 -1.231 2.206 -5.950 1.00 0.00 A N
ATOM 825 CA DILEA 53 -0.320 3.283 -5.652 1.00 0.00 A C
ATOM 826 C DILEA 53 0.780 3.254 -6.714 1.00 0.00 A C
ATOM 827 O DILEA 53 0.600 3.777 -7.810 1.00 0.00 A O
ATOM 828 CB DILEA 53 -1.107 4.615 -5.630 1.00 0.00 A C
ATOM 829 CG1 DILEA 53 -2.270 4.512 -4.587 1.00 0.00 A C
ATOM 830 CG2 DILEA 53 -0.184 5.769 -5.315 1.00 0.00 A C
ATOM 831 CD1 DILEA 53 -3.276 5.653 -4.618 1.00 0.00 A C
ATOM 832 H DILEA 53 -1.848 2.298 -6.741 1.00 0.00 A H
ATOM 833 HA DILEA 53 0.206 3.086 -4.723 1.00 0.00 A H
ATOM 834 HB DILEA 53 -1.563 4.775 -6.595 1.00 0.00 A H
ATOM 835 1HG1 DILEA 53 -1.853 4.479 -3.616 1.00 0.00 A H
ATOM 836 2HG1 DILEA 53 -2.808 3.585 -4.760 1.00 0.00 A H
ATOM 837 1HG2 DILEA 53 -0.742 6.702 -5.307 1.00 0.00 A H
ATOM 838 2HG2 DILEA 53 0.567 5.810 -6.071 1.00 0.00 A H
ATOM 839 3HG2 DILEA 53 0.280 5.622 -4.346 1.00 0.00 A H
ATOM 840 1HD1 DILEA 53 -4.038 5.487 -3.856 1.00 0.00 A H
ATOM 841 2HD1 DILEA 53 -3.752 5.688 -5.594 1.00 0.00 A H
ATOM 842 3HD1 DILEA 53 -2.774 6.598 -4.422 1.00 0.00 A H
ATOM 843 N DARGA 54 1.926 2.636 -6.379 1.00 0.00 A N
ATOM 844 CA DARGA 54 3.029 2.454 -7.329 1.00 0.00 A C
ATOM 845 C DARGA 54 4.093 3.521 -7.174 1.00 0.00 A C
ATOM 846 O DARGA 54 4.984 3.405 -6.337 1.00 0.00 A O
ATOM 847 CB DARGA 54 3.706 1.107 -7.139 1.00 0.00 A C
ATOM 848 CG DARGA 54 2.843 -0.095 -7.346 1.00 0.00 A C
ATOM 849 CD DARGA 54 3.616 -1.343 -7.154 1.00 0.00 A C
ATOM 850 NE DARGA 54 2.788 -2.506 -7.290 1.00 0.00 A N
ATOM 851 CZ DARGA 54 3.199 -3.781 -7.184 1.00 0.00 A C
ATOM 852 NH1 DARGA 54 4.459 -4.063 -6.935 1.00 0.00 A N
ATOM 853 NH2 DARGA 54 2.311 -4.748 -7.333 1.00 0.00 A N
ATOM 854 H DARGA 54 2.060 2.270 -5.443 1.00 0.00 A H
ATOM 855 HA DARGA 54 2.635 2.547 -8.342 1.00 0.00 A H
ATOM 856 1HB DARGA 54 4.126 1.046 -6.142 1.00 0.00 A H
ATOM 857 2HB DARGA 54 4.534 1.030 -7.840 1.00 0.00 A H
ATOM 858 1HG DARGA 54 2.418 -0.087 -8.350 1.00 0.00 A H
ATOM 859 2HG DARGA 54 2.043 -0.083 -6.605 1.00 0.00 A H
ATOM 860 1HD DARGA 54 4.034 -1.345 -6.165 1.00 0.00 A H
ATOM 861 2HD DARGA 54 4.415 -1.400 -7.890 1.00 0.00 A H
ATOM 862 HE DARGA 54 1.814 -2.353 -7.478 1.00 0.00 A H
ATOM 863 1HH1 DARGA 54 5.131 -3.317 -6.821 1.00 0.00 A H
ATOM 864 2HH1 DARGA 54 4.755 -5.025 -6.858 1.00 0.00 A H
ATOM 865 1HH2 DARGA 54 1.342 -4.500 -7.522 1.00 0.00 A H
ATOM 866 2HH2 DARGA 54 2.592 -5.714 -7.259 1.00 0.00 A H
ATOM 867 N DLEUA 55 4.023 4.570 -7.967 1.00 0.00 A N
ATOM 868 CA DLEUA 55 4.986 5.634 -7.786 1.00 0.00 A C
ATOM 869 C DLEUA 55 5.936 5.691 -8.971 1.00 0.00 A C
ATOM 870 O DLEUA 55 5.496 5.564 -10.108 1.00 0.00 A O
ATOM 871 CB DLEUA 55 4.253 6.952 -7.633 1.00 0.00 A C
ATOM 872 CG DLEUA 55 3.260 6.992 -6.554 1.00 0.00 A C
ATOM 873 CD1 DLEUA 55 2.543 8.307 -6.629 1.00 0.00 A C
ATOM 874 CD2 DLEUA 55 3.939 6.793 -5.201 1.00 0.00 A C
ATOM 875 H DLEUA 55 3.322 4.656 -8.695 1.00 0.00 A H
ATOM 876 HA DLEUA 55 5.581 5.424 -6.902 1.00 0.00 A H
ATOM 877 1HB DLEUA 55 3.728 7.155 -8.548 1.00 0.00 A H
ATOM 878 2HB DLEUA 55 4.966 7.741 -7.455 1.00 0.00 A H
ATOM 879 HG DLEUA 55 2.549 6.203 -6.718 1.00 0.00 A H
ATOM 880 1HD1 DLEUA 55 1.779 8.344 -5.870 1.00 0.00 A H
ATOM 881 2HD1 DLEUA 55 2.080 8.407 -7.611 1.00 0.00 A H
ATOM 882 3HD1 DLEUA 55 3.252 9.117 -6.476 1.00 0.00 A H
ATOM 883 1HD2 DLEUA 55 3.188 6.814 -4.419 1.00 0.00 A H
ATOM 884 2HD2 DLEUA 55 4.661 7.592 -5.035 1.00 0.00 A H
ATOM 885 3HD2 DLEUA 55 4.452 5.833 -5.180 1.00 0.00 A H
ATOM 886 N DASNA 56 7.228 5.882 -8.707 1.00 0.00 A N
ATOM 887 CA DASNA 56 8.226 5.998 -9.768 1.00 0.00 A C
ATOM 888 C DASNA 56 9.120 7.225 -9.587 1.00 0.00 A C
ATOM 889 O DASNA 56 9.602 7.517 -8.492 1.00 0.00 A O
ATOM 890 CB DASNA 56 9.052 4.731 -9.895 1.00 0.00 A C
ATOM 891 CG DASNA 56 8.269 3.603 -10.539 1.00 0.00 A C
ATOM 892 ND2 DASNA 56 7.807 2.660 -9.765 1.00 0.00 A N
ATOM 893 OD1 DASNA 56 8.098 3.601 -11.763 1.00 0.00 A O
ATOM 894 OXT DASNA 56 9.360 7.934 -10.562 1.00 0.00 A O
ATOM 895 H DASNA 56 7.530 5.947 -7.746 1.00 0.00 A H
ATOM 896 HA DASNA 56 7.707 6.125 -10.716 1.00 0.00 A H
ATOM 897 1HB DASNA 56 9.383 4.411 -8.910 1.00 0.00 A H
ATOM 898 2HB DASNA 56 9.942 4.932 -10.490 1.00 0.00 A H
ATOM 899 1HD2 DASNA 56 7.289 1.900 -10.159 1.00 0.00 A H
ATOM 900 2HD2 DASNA 56 7.975 2.688 -8.785 1.00 0.00 A H

I tried using a pdb file with the chain column removed entirely, with the spacing preserved, but pdb2gmx then identifies my C-terminal residue as Gly 51 rather than 56. I’m not sure if I could get around this internal break by using -merge in pdb2gmx? Will -merge make the correct amide linkage between 51 and 52, and let me choose 56 as COO-?

Thank you!

2

The concept of type is key for Gromacs because it has to know e.g. whether to connect two residues by a peptide bond (if they are amino acids) or not. Residue types are defined in (appropriately named) residuetypes.dat, located in the general force field directory for Gromacs.

You can make a local copy of residuetypes.dat and define these residues as Protein - in fact, CHARMM36 has residue definitions for D-amino acids that are almost identical to L-amino acids, except for a few backbone atom types (I think the dihedral terms might be identical, but CMAPs not necessarily so). This way pdb2gmx will use the local copy of residuetypes.dat to determine how to connect consecutive residues.

3

Thank you for the suggestion!

I copied residuetypes.dat into my charmm36_ljpme-jul2022.ff folder and added the following lines:

DARG Protein
DLYS Protein
DILE Protein
DPHE Protein
DLEU Protein
DTRP Protein
DMET Protein
DPRO Protein
DCYS Protein
DASN Protein
DVAL Protein
DSER Protein
DGLN Protein
DTYR Protein
DASP Protein
DGLU Protein
DTHR Protein

I’m assuming that when I use -ff with pdb2gmx the program will find the residuetypes.dat file in this folder?

I removed the chain ID from my D-residues in the pdb file, as pdb2gmx reads it as DXXXA when I want just DXXX, see below:
ATOM 387 N DPHE 51 -6.334 -1.841 -3.860 1.00 0.00 A N
ATOM 388 CA DPHE 51 -5.165 -1.020 -3.543 1.00 0.00 A C
ATOM 389 C DPHE 51 -4.285 -0.813 -4.725 1.00 0.00 A C
ATOM 390 O DPHE 51 -4.666 -1.120 -5.836 1.00 0.00 A O
ATOM 391 CB DPHE 51 -5.448 0.350 -2.879 1.00 0.00 A C
ATOM 392 CG DPHE 51 -6.279 1.381 -3.540 1.00 0.00 A C
ATOM 393 CD1 DPHE 51 -5.717 2.308 -4.424 1.00 0.00 A C
ATOM 394 CD2 DPHE 51 -7.586 1.514 -3.196 1.00 0.00 A C
ATOM 395 CE1 DPHE 51 -6.486 3.333 -4.945 1.00 0.00 A C

Using the following command: gmx pdb2gmx -f 2GB1_Rip_R_0131_3.pdb -ff charmm36_ljpme-jul2022 -o 2GB1_131.gro -ignh -merge interactive

I am able to merge chain ‘A’ (L- residues) and chain ’ ’ (D-residues) but still end up with a false chain termination, and error related to the C-terminal patch of DASN?

Section of pdb2gmx output:

Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.

Merge chain ending with residue GLY50 (chain id ‘A’, atom 386 O) and chain starting with residue DPHE51 (chain id ’ ', atom 387 N) into a single moleculetype (keeping termini)? [n/y]
y

Merged chains into joint molecule definitions at 1 places.

There are 1 chains and 0 blocks of water and 56 residues with 442 atoms

** chain #res #atoms**

** 1 ‘A’ 56 442**

All occupancies are one
All occupancies are one
Opening force field file ./charmm36_ljpme-jul2022.ff/atomtypes.atp

Reading residue database… (Charmm36_ljpme-jul2022)
Opening force field file ./charmm36_ljpme-jul2022.ff/aminoacids.rtp
Opening force field file ./charmm36_ljpme-jul2022.ff/carb.rtp
Opening force field file ./charmm36_ljpme-jul2022.ff/cgenff.rtp
Opening force field file ./charmm36_ljpme-jul2022.ff/ethers.rtp
Opening force field file ./charmm36_ljpme-jul2022.ff/lipid.rtp
Opening force field file ./charmm36_ljpme-jul2022.ff/metals.rtp
Opening force field file ./charmm36_ljpme-jul2022.ff/na.rtp
Opening force field file ./charmm36_ljpme-jul2022.ff/silicates.rtp
Opening force field file ./charmm36_ljpme-jul2022.ff/solvent.rtp
Opening force field file ./charmm36_ljpme-jul2022.ff/aminoacids.hdb
Opening force field file ./charmm36_ljpme-jul2022.ff/carb.hdb
Opening force field file ./charmm36_ljpme-jul2022.ff/cgenff.hdb
Opening force field file ./charmm36_ljpme-jul2022.ff/ethers.hdb
Opening force field file ./charmm36_ljpme-jul2022.ff/lipid.hdb
Opening force field file ./charmm36_ljpme-jul2022.ff/metals.hdb
Opening force field file ./charmm36_ljpme-jul2022.ff/na.hdb
Opening force field file ./charmm36_ljpme-jul2022.ff/silicates.hdb
Opening force field file ./charmm36_ljpme-jul2022.ff/solvent.hdb
Opening force field file ./charmm36_ljpme-jul2022.ff/aminoacids.n.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/carb.n.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/cgenff.n.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/ethers.n.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/lipid.n.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/metals.n.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/na.n.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/silicates.n.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/solvent.n.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/aminoacids.c.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/carb.c.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/cgenff.c.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/ethers.c.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/lipid.c.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/metals.c.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/na.c.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/silicates.c.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/solvent.c.tdb

Back Off! I just backed up topol.top to ./#topol.top.7#

Processing chain 1 ‘A’ (442 atoms, 56 residues)

Identified residue LEU1 as a starting terminus.

Identified residue GLY50 as a ending terminus.
9 out of 9 lines of specbond.dat converted successfully
Start terminus LEU-1: NH3+
End terminus GLY-50: COO-
Opening force field file ./charmm36_ljpme-jul2022.ff/aminoacids.arn

Program: gmx pdb2gmx, version 2024.1
Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 870)

Fatal error:
Atom OXT in residue DASN 56 was not found in rtp entry DASN with 14 atoms
while sorting atoms.

4

Be careful here - seems now you have your chain “A” in the PDB only assigned to residues 1-50, so pdb2gmx will anyway consider Gly-50 as the terminal residue and split it into two polypeptide entities within one container. Keep these "A"s in your D-residues, just make sure they’re at the correct position in the (fixed) PDB format, and check for the End terminus notification in the output. There’s no problem with having a DXXXA string because PDB assigns up to 4 letters for the residue name and 1 letter for the chain.

The final error relates to the fact that you have the extra oxygen in the initial structure, and pdb2gmx wants to add a patch on top of that. It should be fine if you just remove OXT from the last residue.

5

No, the file need to be in the working directory (where pdb2gmx will look first) or in $GMXLIB. It will not search within force field subdirectories.

6

Restoring the chain id to A for all residues, and moving my residuetypes.dat file to my working directory appears to have solved my issue! - Thank you, All!

pdb2gmx found all 56 residues in the chain and correctly applied my desired N and C terminal patches

Processing chain 1 ‘A’ (442 atoms, 56 residues)

Identified residue LEU1 as a starting terminus.

Identified residue DASN56 as a ending terminus.
9 out of 9 lines of specbond.dat converted successfully
Start terminus LEU-1: NH3+
End terminus DASN-56: COO-
Opening force field file ./charmm36_ljpme-jul2022.ff/aminoacids.arn

Checking for duplicate atoms…

Generating any missing hydrogen atoms and/or adding termini.

Now there are 56 residues with 900 atoms

Making bonds…

Number of bonds was 905, now 905

Generating angles, dihedrals and pairs…
Before cleaning: 2382 pairs
Before cleaning: 2387 dihedrals

Making cmap torsions…

There are 54 cmap torsion pairs

There are 2387 dihedrals, 153 impropers, 1637 angles
2367 pairs, 905 bonds and 0 virtual sites

Total mass 6261.236 a.m.u.

Total charge 2.000 e

Writing topology

Writing coordinate file…

	--------- PLEASE NOTE ------------

You have successfully generated a topology from: 2GB1_Rip_R_0131_2.pdb.

The Charmm36_ljpme-jul2022 force field and the tip3p water model are used.

	--------- ETON ESAELP ------------

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