Help creating and using one topology file for multiple non-standard amino acids

IsovalineDude · February 6, 2026, 7:56am

I’m trying to dock a peptide containing non-standard D-amino acids (D-Serine/DSN and D-Isovaline/DIV) to a protein using HADDOCK3, but the topology generation is silently failing for the peptide while succeeding for the receptor.

What Works ✓

L-peptide with single non-standard residue (IVA - L-Isovaline) docks successfully

Configuration:

run_dir = "run_L_peptide"
ncores = 2
clean = false

molecules = [
    "receptor.pdb",
    "maestro_L_peptide_chainB.pdb"
    ]

[topoaa]
ligand_param_fname = "./iva.par"
ligand_top_fname = "./iva.top"
log_level = "verbose"

[rigidbody]
sampling = 20
ambig_fname = "restraints_maestro.tbl"
ligand_param_fname = "./iva.par"
ligand_top_fname = "./iva.top"

[caprieval]

[clustfcc]
clust_cutoff = 0.6

Result: All 5 residues present in final structure (SER-TRP-LEU-THR-IVA), full workflow completes successfully.

What Doesn’t Work ✗

D-peptide with TWO non-standard residues (DSN and DIV)

Peptide structure: DSN(HETATM)-TRP(ATOM)-LEU(ATOM)-THR(ATOM)-DIV(HETATM)

Configuration:

run_dir = "run_D_peptide"
ncores = 2
clean = false

molecules = [
    "receptor.pdb",
    "maestro_D_peptide_chainB.pdb"
    ]

[topoaa]
ligand_param_fname = "./combined_fixed.par"
ligand_top_fname = "./combined_fixed.top"
log_level = "verbose"
tolerance = 50

[rigidbody]
sampling = 20
ambig_fname = "restraints_maestro.tbl"
ligand_param_fname = "./combined_fixed.par"
ligand_top_fname = "./combined_fixed.top"

[caprieval]

[clustfcc]
clust_cutoff = 0.6

Error Output

[topoaa] CNS jobs have finished
50.00% of output was not generated for this module and tolerance was set to 0.00%.

With tolerance = 50:

[topoaa] Module [topoaa] finished.
[rigidbody] Running [rigidbody] module
ERROR: division by zero
ZeroDivisionError: division by zero
    sampling_factor = int(self.params["sampling"] / len(models_to_dock))

Result: Only receptor PDB generated, peptide silently fails. No CNS error files despite clean=false.

File Contents

1. Working IVA Topology (iva.top)

Click to expand iva.top

Remarks iva_clean_CNS.top created by acpype (v: 2023.10.27)

set echo=false end

autogenerate angles=True dihedrals=True end

{ atomType  mass }
MASS NT_     14.010
MASS CT_     12.010
MASS C_      12.010
MASS O_      16.000
MASS OH_     16.000
MASS H_       1.008
MASS HO_      1.008
MASS HC_      1.008

RESIdue IVA

GROUP

{ atomName  atomType  Charge }
ATOM N     TYPE= NT_   CHARGE=  -0.8948 END
ATOM CA    TYPE= CT_   CHARGE=   0.1592 END
ATOM C     TYPE= C_    CHARGE=   0.5871 END
ATOM O     TYPE= O_    CHARGE=  -0.5650 END
ATOM O1    TYPE= OH_   CHARGE=  -0.5991 END
ATOM C1    TYPE= CT_   CHARGE=  -0.0881 END
ATOM C2    TYPE= CT_   CHARGE=  -0.1021 END
ATOM C3    TYPE= CT_   CHARGE=  -0.0744 END
ATOM H     TYPE= H_    CHARGE=   0.3648 END
ATOM H1    TYPE= HO_   CHARGE=   0.4420 END
ATOM H2    TYPE= HC_   CHARGE=   0.0534 END
ATOM H3    TYPE= HC_   CHARGE=   0.0534 END
ATOM H4    TYPE= HC_   CHARGE=   0.0534 END
ATOM H5    TYPE= HC_   CHARGE=   0.0427 END
ATOM H6    TYPE= HC_   CHARGE=   0.0427 END
ATOM H7    TYPE= HC_   CHARGE=   0.0427 END
ATOM H8    TYPE= HC_   CHARGE=   0.0587 END
ATOM H9    TYPE= HC_   CHARGE=   0.0587 END
ATOM H10   TYPE= H_    CHARGE=   0.3648 END

{ Bonds: atomName1  atomName2 }
BOND N     H    
BOND N     H10  
BOND O1    H1   
BOND C1    H3   
BOND C1    H4   
BOND C1    H2   
BOND C2    H7   
BOND C2    H6   
BOND C2    H5   
BOND C3    H9   
BOND C3    H8   
BOND N     CA   
BOND CA    C1   
BOND CA    C    
BOND CA    C3   
BOND C     O1   
BOND C     O    
BOND C2    C3   

{ Angles: atomName1 atomName2 atomName3}
ANGLe CA    N     H    
ANGLe CA    N     H10  
ANGLe CA    C1    H3   
ANGLe CA    C1    H4   
ANGLe CA    C1    H2   
ANGLe CA    C3    H9   
ANGLe CA    C3    H8   
ANGLe C     O1    H1   
ANGLe C2    C3    H9   
ANGLe C2    C3    H8   
ANGLe C3    C2    H7   
ANGLe C3    C2    H6   
ANGLe C3    C2    H5   
ANGLe H     N     H10  
ANGLe H2    C1    H3   
ANGLe H2    C1    H4   
ANGLe H3    C1    H4   
ANGLe H5    C2    H7   
ANGLe H5    C2    H6   
ANGLe H6    C2    H7   
ANGLe H8    C3    H9   
ANGLe N     CA    C1   
ANGLe N     CA    C    
ANGLe N     CA    C3   
ANGLe CA    C     O1   
ANGLe CA    C     O    
ANGLe CA    C3    C2   
ANGLe C     CA    C1   
ANGLe C     CA    C3   
ANGLe O     C     O1   
ANGLe C1    CA    C3   

{ Proper Dihedrals: name1 name2 name3 name4 }
DIHEdral N     CA    C1    H3   
DIHEdral N     CA    C1    H4   
DIHEdral N     CA    C1    H2   
DIHEdral N     CA    C3    H9   
DIHEdral N     CA    C3    H8   
DIHEdral CA    C     O1    H1   
DIHEdral CA    C3    C2    H7   
DIHEdral CA    C3    C2    H6   
DIHEdral CA    C3    C2    H5   
DIHEdral H     N     CA    C    
DIHEdral H10   N     CA    C    
DIHEdral C     CA    C1    H3   
DIHEdral C     CA    C1    H4   
DIHEdral C     CA    C1    H2   
DIHEdral C     CA    C3    H9   
DIHEdral C     CA    C3    H8   
DIHEdral O     C     O1    H1   
DIHEdral H     N     CA    C1   
DIHEdral H10   N     CA    C1   
DIHEdral C1    CA    C3    H9   
DIHEdral C1    CA    C3    H8   
DIHEdral H     N     CA    C3   
DIHEdral H10   N     CA    C3   
DIHEdral C3    CA    C1    H3   
DIHEdral C3    CA    C1    H4   
DIHEdral C3    CA    C1    H2   
DIHEdral H5    C2    C3    H9   
DIHEdral H5    C2    C3    H8   
DIHEdral H6    C2    C3    H9   
DIHEdral H6    C2    C3    H8   
DIHEdral H7    C2    C3    H9   
DIHEdral H7    C2    C3    H8   
DIHEdral N     CA    C     O1   
DIHEdral N     CA    C     O    
DIHEdral N     CA    C3    C2   
DIHEdral C     CA    C3    C2   
DIHEdral O     C     CA    C1   
DIHEdral O     C     CA    C3   
DIHEdral O1    C     CA    C1   
DIHEdral O1    C     CA    C3   
DIHEdral C1    CA    C3    C2   

{ Improper Dihedrals: aName1 aName2 aName3 aName4 }
IMPRoper CA    O     C     O1   
IMPRoper N     C3    C     C1   

END {RESIdue IVA}

set echo=true end

2. Non-Working Combined DSN+DIV Topology (combined_fixed.top)

Click to expand combined_fixed.top (first 150 lines)

Remarks Combined DSN and DIV topologies from acpype

set echo=false end

autogenerate angles=True dihedrals=True end

{ atomType  mass }
MASS NT_     14.010
MASS CT_     12.010
MASS C_      12.010
MASS O_      16.000
MASS OH_     16.000
MASS H_       1.008
MASS H1_      1.008
MASS HO_      1.008
MASS HC_      1.008

RESIdue DSN

GROUP

{ atomName  atomType  Charge }
ATOM N     TYPE= NT_   CHARGE=  -0.8868 END
ATOM CA    TYPE= CT_   CHARGE=   0.0425 END
ATOM C     TYPE= C_    CHARGE=   0.5309 END
ATOM O     TYPE= O_    CHARGE=  -0.5371 END
ATOM CB    TYPE= CT_   CHARGE=   0.1364 END
ATOM OG    TYPE= OH_   CHARGE=  -0.6098 END
ATOM H1    TYPE= H_    CHARGE=   0.3573 END
ATOM H2    TYPE= H_    CHARGE=   0.3573 END
ATOM HB2   TYPE= H1_   CHARGE=   0.0392 END
ATOM HB3   TYPE= H1_   CHARGE=   0.0392 END
ATOM HG    TYPE= HO_   CHARGE=   0.4100 END
ATOM HA    TYPE= H1_   CHARGE=   0.0957 END

{ Bonds: atomName1  atomName2 }
BOND N     H1   
BOND N     H2   
BOND CA    HA   
BOND CB    HB2  
BOND CB    HB3  
BOND OG    HG   
BOND N     CA   
BOND CA    CB   
BOND CA    C    
BOND C     O    
BOND CB    OG   

{ Angles: atomName1 atomName2 atomName3}
ANGLe N     CA    HA   
ANGLe CA    N     H1   
ANGLe CA    N     H2   
ANGLe CA    CB    HB2  
ANGLe CA    CB    HB3  
ANGLe C     CA    HA   
ANGLe CB    CA    HA   
ANGLe CB    OG    HG   
ANGLe OG    CB    HB2  
ANGLe OG    CB    HB3  
ANGLe H1    N     H2   
ANGLe HB2   CB    HB3  
ANGLe N     CA    CB   
ANGLe N     CA    C    
ANGLe CA    CB    OG   
ANGLe CA    C     O    
ANGLe C     CA    CB   

{ Proper Dihedrals: name1 name2 name3 name4 }
DIHEdral N     CA    CB    HB2  
DIHEdral N     CA    CB    HB3  
DIHEdral CA    CB    OG    HG   
DIHEdral H1    N     CA    C    
DIHEdral H2    N     CA    C    
DIHEdral C     CA    CB    HB2  
DIHEdral C     CA    CB    HB3  
DIHEdral O     C     CA    HA   
DIHEdral H1    N     CA    CB   
DIHEdral H2    N     CA    CB   
DIHEdral OG    CB    CA    HA   
DIHEdral H1    N     CA    HA   
DIHEdral H2    N     CA    HA   
DIHEdral HB2   CB    CA    HA   
DIHEdral HB2   CB    OG    HG   
DIHEdral HB3   CB    CA    HA   
DIHEdral HB3   CB    OG    HG   
DIHEdral N     CA    CB    OG   
DIHEdral N     CA    C     O    
DIHEdral C     CA    CB    OG   
DIHEdral O     C     CA    CB   

{ Improper Dihedrals: aName1 aName2 aName3 aName4 }
IMPRoper HA    N     CB    C    

END

RESIdue DIV

GROUP

{ atomName  atomType  Charge }
ATOM N     TYPE= NT_   CHARGE=  -0.8938 END
ATOM CA    TYPE= CT_   CHARGE=   0.1592 END
ATOM C     TYPE= C_    CHARGE=   0.5871 END
ATOM O     TYPE= O_    CHARGE=  -0.5650 END
ATOM O1    TYPE= OH_   CHARGE=  -0.5991 END
ATOM C1    TYPE= CT_   CHARGE=  -0.0881 END
ATOM C2    TYPE= CT_   CHARGE=  -0.1021 END
ATOM C3    TYPE= CT_   CHARGE=  -0.0744 END
ATOM H     TYPE= H_    CHARGE=   0.3648 END
ATOM H1    TYPE= HO_   CHARGE=   0.4420 END
ATOM H2    TYPE= HC_   CHARGE=   0.0534 END
ATOM H3    TYPE= HC_   CHARGE=   0.0534 END
ATOM H4    TYPE= HC_   CHARGE=   0.0534 END
ATOM H5    TYPE= HC_   CHARGE=   0.0427 END
ATOM H6    TYPE= HC_   CHARGE=   0.0427 END
ATOM H7    TYPE= HC_   CHARGE=   0.0427 END
ATOM H8    TYPE= HC_   CHARGE=   0.0587 END
ATOM H9    TYPE= HC_   CHARGE=   0.0587 END
ATOM H10   TYPE= H_    CHARGE=   0.3648 END

{ Bonds: atomName1  atomName2 }
BOND N     H    
BOND N     H10  
BOND O1    H1   
BOND C1    H3   
BOND C1    H4   
BOND C1    H2   
BOND C2    H7   
BOND C2    H6   
BOND C2    H5   
BOND C3    H9   
BOND C3    H8   
BOND N     CA   
BOND CA    C1   
BOND CA    C    
BOND CA    C3   
BOND C     O1   
BOND C     O    
BOND C2    C3   

[...continues with DIV angles, dihedrals, impropers...]

END

set echo=true end

3. PDB File Comparison

Maestro L-peptide (working):

TITLE     rb-1-L_Maestro
REMARK   4      COMPLIES WITH FORMAT V. 3.0, 1-DEC-2006
REMARK 888
REMARK 888 WRITTEN BY MAESTRO (A PRODUCT OF SCHRODINGER, LLC)
ATOM      1  N   SER B   1       0.751   0.274   6.773  1.00  0.00           N  
ATOM      2  CA  SER B   1       1.031   1.270   5.754  1.00  0.00           C  
ATOM      3  C   SER B   1       2.350   0.946   5.033  1.00  0.00           C  
ATOM      4  O   SER B   1       3.015  -0.041   5.339  1.00  0.00           O  
ATOM      5  CB  SER B   1       1.050   2.629   6.465  1.00  0.00           C  
ATOM      6  OG  SER B   1       1.323   3.670   5.519  1.00  0.00           O  
ATOM      7  H   SER B   1       1.435  -0.463   6.860  1.00  0.00           H  
ATOM      8  HA  SER B   1       0.195   1.323   5.057  1.00  0.00           H  
ATOM      9  HB2 SER B   1       0.080   2.810   6.928  1.00  0.00           H  
ATOM     10  HB3 SER B   1       1.824   2.628   7.232  1.00  0.00           H  
ATOM     11  HG  SER B   1       1.333   4.518   5.970  1.00  0.00           H  
ATOM     12  H   SER B   1       0.697   0.722   7.676  1.00  0.00           H  
ATOM     13  N   TRP B   2       2.715   1.833   4.040  1.00  0.00           N  
ATOM     14  CA  TRP B   2       3.931   1.687   3.252  1.00  0.00           C  
ATOM     15  C   TRP B   2       4.035   2.838   2.239  1.00  0.00           C  
ATOM     16  O   TRP B   2       3.168   3.711   2.177  1.00  0.00           O  
ATOM     17  CB  TRP B   2       3.934   0.296   2.597  1.00  0.00           C  
ATOM     18  CG  TRP B   2       5.110  -0.053   1.737  1.00  0.00           C  
ATOM     19  CD1 TRP B   2       6.245  -0.648   2.169  1.00  0.00           C  
ATOM     20  CD2 TRP B   2       5.282   0.163   0.304  1.00  0.00           C  
ATOM     21  NE1 TRP B   2       7.108  -0.808   1.102  1.00  0.00           N  
ATOM     22  CE2 TRP B   2       6.567  -0.324  -0.070  1.00  0.00           C  
ATOM     23  CE3 TRP B   2       4.486   0.715  -0.719  1.00  0.00           C  
ATOM     24  CZ2 TRP B   2       7.041  -0.258  -1.390  1.00  0.00           C  
ATOM     25  CZ3 TRP B   2       4.948   0.791  -2.045  1.00  0.00           C  
ATOM     26  CH2 TRP B   2       6.223   0.306  -2.383  1.00  0.00           C  
ATOM     27  H   TRP B   2       2.127   2.628   3.833  1.00  0.00           H  
ATOM     28  HA  TRP B   2       4.791   1.625   3.918  1.00  0.00           H  
ATOM     29  HB2 TRP B   2       3.903  -0.471   3.372  1.00  0.00           H  
ATOM     30  HB3 TRP B   2       3.062   0.195   1.952  1.00  0.00           H  
ATOM     31  HD1 TRP B   2       6.353  -0.914   3.211  1.00  0.00           H  
ATOM     32  HE1 TRP B   2       8.011  -1.237   1.243  1.00  0.00           H  
ATOM     33  HE3 TRP B   2       3.499   1.091  -0.491  1.00  0.00           H  
ATOM     34  HZ2 TRP B   2       8.022  -0.638  -1.630  1.00  0.00           H  
ATOM     35  HZ3 TRP B   2       4.321   1.222  -2.812  1.00  0.00           H  
ATOM     36  HH2 TRP B   2       6.576   0.367  -3.402  1.00  0.00           H  
ATOM     37  N   LEU B   3       5.150   2.814   1.426  1.00  0.00           N  
ATOM     38  CA  LEU B   3       5.434   3.808   0.407  1.00  0.00           C  
ATOM     39  C   LEU B   3       6.751   3.414  -0.256  1.00  0.00           C  
ATOM     40  O   LEU B   3       7.346   2.403   0.121  1.00  0.00           O  
ATOM     41  CB  LEU B   3       5.416   5.254   0.974  1.00  0.00           C  
ATOM     42  CG  LEU B   3       5.691   6.482   0.071  1.00  0.00           C  
ATOM     43  CD1 LEU B   3       4.746   6.542  -1.126  1.00  0.00           C  
ATOM     44  CD2 LEU B   3       5.612   7.776   0.880  1.00  0.00           C  
ATOM     45  H   LEU B   3       5.829   2.072   1.522  1.00  0.00           H  
ATOM     46  HA  LEU B   3       4.578   3.897  -0.262  1.00  0.00           H  
ATOM     47  HB2 LEU B   3       4.432   5.469   1.391  1.00  0.00           H  
ATOM     48  HB3 LEU B   3       6.170   5.348   1.755  1.00  0.00           H  
ATOM     49  HG  LEU B   3       6.732   6.472  -0.249  1.00  0.00           H  
ATOM     50 HD11 LEU B   3       4.977   7.420  -1.729  1.00  0.00           H  
ATOM     51 HD12 LEU B   3       4.868   5.644  -1.732  1.00  0.00           H  
ATOM     52 HD13 LEU B   3       3.716   6.605  -0.774  1.00  0.00           H  
ATOM     53 HD21 LEU B   3       5.808   8.626   0.227  1.00  0.00           H  
ATOM     54 HD22 LEU B   3       4.617   7.874   1.314  1.00  0.00           H  
ATOM     55 HD23 LEU B   3       6.354   7.753   1.678  1.00  0.00           H  
ATOM     56  N   THR B   4       7.198   4.244  -1.264  1.00  0.00           N  
ATOM     57  CA  THR B   4       8.427   4.031  -2.008  1.00  0.00           C  
ATOM     58  C   THR B   4       8.551   5.171  -3.026  1.00  0.00           C  
ATOM     59  O   THR B   4       7.678   6.040  -3.081  1.00  0.00           O  
ATOM     60  CB  THR B   4       8.465   2.626  -2.650  1.00  0.00           C  
ATOM     61  OG1 THR B   4       8.345   1.639  -1.619  1.00  0.00           O  
ATOM     62  CG2 THR B   4       9.746   2.354  -3.447  1.00  0.00           C  
ATOM     63  H   THR B   4       6.660   5.058  -1.523  1.00  0.00           H  
ATOM     64  HA  THR B   4       9.264   3.952  -1.314  1.00  0.00           H  
ATOM     65  HB  THR B   4       7.652   2.533  -3.370  1.00  0.00           H  
ATOM     66  HG1 THR B   4       8.368   0.763  -2.010  1.00  0.00           H  
ATOM     67 HG21 THR B   4       9.705   1.350  -3.870  1.00  0.00           H  
ATOM     68 HG22 THR B   4       9.835   3.083  -4.253  1.00  0.00           H  
ATOM     69 HG23 THR B   4      10.610   2.435  -2.788  1.00  0.00           H  
TER      70      THR A   4
HETATM   71  N   IVA B   5       9.668   5.142  -3.836  1.00  0.00           N  
HETATM   72  CA  IVA B   5       9.932   6.157  -4.858  1.00  0.00           C  
HETATM   73  C   IVA B   5      11.252   5.823  -5.571  1.00  0.00           C  
HETATM   74  O   IVA B   5      11.912   4.833  -5.260  1.00  0.00           O  
HETATM   75  O1  IVA B   5      11.621   6.693  -6.554  1.00  0.00           O  
HETATM   76  C1  IVA B   5       8.718   6.285  -5.774  1.00  0.00           C  
HETATM   77  C2  IVA B   5      10.143   8.742  -5.218  1.00  0.00           C  
HETATM   78  C3  IVA B   5       9.882   7.559  -4.256  1.00  0.00           C  
HETATM   79  H   IVA B   5      10.344   4.399  -3.738  1.00  0.00           H  
HETATM   80  H1  IVA B   5      12.449   6.363  -6.904  1.00  0.00           H  
HETATM   81  H2  IVA B   5       7.817   6.523  -5.208  1.00  0.00           H  
HETATM   82  H3  IVA B   5       8.849   7.069  -6.523  1.00  0.00           H  
HETATM   83  H4  IVA B   5       8.522   5.356  -6.312  1.00  0.00           H  
HETATM   84  H5  IVA B   5      10.072   9.692  -4.687  1.00  0.00           H  
HETATM   85  H6  IVA B   5      11.138   8.694  -5.659  1.00  0.00           H  
HETATM   86  H7  IVA B   5       9.416   8.771  -6.031  1.00  0.00           H  
HETATM   87  H8  IVA B   5      10.598   7.618  -3.433  1.00  0.00           H  
HETATM   88  H9  IVA B   5       8.906   7.703  -3.789  1.00  0.00           H  
CONECT   71   58   72   79
CONECT   72   71   73   76   78
CONECT   73   72   74   75
CONECT   73   74
CONECT   74   73
CONECT   74   73
CONECT   79   71
CONECT   75   73   80
CONECT   80   75
CONECT   76   72   81   82   83
CONECT   81   76
CONECT   82   76
CONECT   83   76
CONECT   77   78   84   85   86
CONECT   78   72   77   87   88
CONECT   84   77
CONECT   85   77
CONECT   86   77
CONECT   87   78
CONECT   88   78
END

Maestro D-peptide (not working):

TITLE     rb-1-D_Maestro
REMARK   4      COMPLIES WITH FORMAT V. 3.0, 1-DEC-2006
REMARK 888
REMARK 888 WRITTEN BY MAESTRO (A PRODUCT OF SCHRODINGER, LLC)
HETATM    1  N   DSN B   1       0.751   0.274   6.773  1.00  0.00           N  
HETATM    2  CA  DSN B   1       1.031   1.270   5.754  1.00  0.00           C  
HETATM    3  C   DSN B   1       2.350   0.946   5.033  1.00  0.00           C  
HETATM    4  O   DSN B   1       3.015  -0.041   5.339  1.00  0.00           O  
HETATM    5  CB  DSN B   1      -0.140   1.345   4.778  1.00  0.00           C  
HETATM    6  OG  DSN B   1       0.128   2.326   3.769  1.00  0.00           O  
HETATM    7  H1  DSN B   1       1.435  -0.463   6.860  1.00  0.00           H  
HETATM    8  H2  DSN B   1       0.697   0.722   7.676  1.00  0.00           H  
HETATM    9  HB2 DSN B   1      -0.282   0.373   4.305  1.00  0.00           H  
HETATM   10  HB3 DSN B   1      -1.045   1.622   5.317  1.00  0.00           H  
HETATM   11  HG  DSN B   1      -0.611   2.368   3.159  1.00  0.00           H  
HETATM   12  HA  DSN B   1       1.044   2.236   6.259  1.00  0.00           H  
ATOM     13  N   TRP B   2       2.715   1.833   4.040  1.00  0.00           N  
ATOM     14  CA  TRP B   2       3.931   1.687   3.252  1.00  0.00           C  
ATOM     15  C   TRP B   2       4.035   2.838   2.239  1.00  0.00           C  
ATOM     16  O   TRP B   2       3.168   3.711   2.177  1.00  0.00           O  
ATOM     17  CB  TRP B   2       3.934   0.296   2.597  1.00  0.00           C  
ATOM     18  CG  TRP B   2       5.110  -0.053   1.737  1.00  0.00           C  
ATOM     19  CD1 TRP B   2       6.245  -0.648   2.169  1.00  0.00           C  
ATOM     20  CD2 TRP B   2       5.282   0.163   0.304  1.00  0.00           C  
ATOM     21  NE1 TRP B   2       7.108  -0.808   1.102  1.00  0.00           N  
ATOM     22  CE2 TRP B   2       6.567  -0.324  -0.070  1.00  0.00           C  
ATOM     23  CE3 TRP B   2       4.486   0.715  -0.719  1.00  0.00           C  
ATOM     24  CZ2 TRP B   2       7.041  -0.258  -1.390  1.00  0.00           C  
ATOM     25  CZ3 TRP B   2       4.948   0.791  -2.045  1.00  0.00           C  
ATOM     26  CH2 TRP B   2       6.223   0.306  -2.383  1.00  0.00           C  
ATOM     27  H   TRP B   2       2.127   2.628   3.833  1.00  0.00           H  
ATOM     28  HA  TRP B   2       4.791   1.625   3.918  1.00  0.00           H  
ATOM     29  HB2 TRP B   2       3.903  -0.471   3.372  1.00  0.00           H  
ATOM     30  HB3 TRP B   2       3.062   0.195   1.952  1.00  0.00           H  
ATOM     31  HD1 TRP B   2       6.353  -0.914   3.211  1.00  0.00           H  
ATOM     32  HE1 TRP B   2       8.011  -1.237   1.243  1.00  0.00           H  
ATOM     33  HE3 TRP B   2       3.499   1.091  -0.491  1.00  0.00           H  
ATOM     34  HZ2 TRP B   2       8.022  -0.638  -1.630  1.00  0.00           H  
ATOM     35  HZ3 TRP B   2       4.321   1.222  -2.812  1.00  0.00           H  
ATOM     36  HH2 TRP B   2       6.576   0.367  -3.402  1.00  0.00           H  
ATOM     37  N   LEU B   3       5.150   2.814   1.426  1.00  0.00           N  
ATOM     38  CA  LEU B   3       5.434   3.808   0.407  1.00  0.00           C  
ATOM     39  C   LEU B   3       6.751   3.414  -0.256  1.00  0.00           C  
ATOM     40  O   LEU B   3       7.346   2.403   0.121  1.00  0.00           O  
ATOM     41  CB  LEU B   3       5.416   5.254   0.974  1.00  0.00           C  
ATOM     42  CG  LEU B   3       5.691   6.482   0.071  1.00  0.00           C  
ATOM     43  CD1 LEU B   3       4.746   6.542  -1.126  1.00  0.00           C  
ATOM     44  CD2 LEU B   3       5.612   7.776   0.880  1.00  0.00           C  
ATOM     45  H   LEU B   3       5.829   2.072   1.522  1.00  0.00           H  
ATOM     46  HA  LEU B   3       4.578   3.897  -0.262  1.00  0.00           H  
ATOM     47  HB2 LEU B   3       4.432   5.469   1.391  1.00  0.00           H  
ATOM     48  HB3 LEU B   3       6.170   5.348   1.755  1.00  0.00           H  
ATOM     49  HG  LEU B   3       6.732   6.472  -0.249  1.00  0.00           H  
ATOM     50 HD11 LEU B   3       4.977   7.420  -1.729  1.00  0.00           H  
ATOM     51 HD12 LEU B   3       4.868   5.644  -1.732  1.00  0.00           H  
ATOM     52 HD13 LEU B   3       3.716   6.605  -0.774  1.00  0.00           H  
ATOM     53 HD21 LEU B   3       5.808   8.626   0.227  1.00  0.00           H  
ATOM     54 HD22 LEU B   3       4.617   7.874   1.314  1.00  0.00           H  
ATOM     55 HD23 LEU B   3       6.354   7.753   1.678  1.00  0.00           H  
ATOM     56  N   THR B   4       7.198   4.244  -1.264  1.00  0.00           N  
ATOM     57  CA  THR B   4       8.427   4.031  -2.008  1.00  0.00           C  
ATOM     58  C   THR B   4       8.551   5.171  -3.026  1.00  0.00           C  
ATOM     59  O   THR B   4       7.678   6.040  -3.081  1.00  0.00           O  
ATOM     60  CB  THR B   4       8.465   2.626  -2.650  1.00  0.00           C  
ATOM     61  OG1 THR B   4       8.345   1.639  -1.619  1.00  0.00           O  
ATOM     62  CG2 THR B   4       9.746   2.354  -3.447  1.00  0.00           C  
ATOM     63  H   THR B   4       6.660   5.058  -1.523  1.00  0.00           H  
ATOM     64  HA  THR B   4       9.264   3.952  -1.314  1.00  0.00           H  
ATOM     65  HB  THR B   4       7.652   2.533  -3.370  1.00  0.00           H  
ATOM     66  HG1 THR B   4       8.368   0.763  -2.010  1.00  0.00           H  
ATOM     67 HG21 THR B   4       9.705   1.350  -3.870  1.00  0.00           H  
ATOM     68 HG22 THR B   4       9.835   3.083  -4.253  1.00  0.00           H  
ATOM     69 HG23 THR B   4      10.610   2.435  -2.788  1.00  0.00           H  
HETATM   70  N   DIV B   5       9.668   5.142  -3.836  1.00  0.00           N  
HETATM   71  CA  DIV B   5       9.932   6.157  -4.858  1.00  0.00           C  
HETATM   72  C   DIV B   5      11.252   5.823  -5.571  1.00  0.00           C  
HETATM   73  O   DIV B   5      11.912   4.833  -5.260  1.00  0.00           O  
HETATM   74  O1  DIV B   5      11.621   6.693  -6.554  1.00  0.00           O  
HETATM   75  C1  DIV B   5       9.882   7.559  -4.256  1.00  0.00           C  
HETATM   76  C2  DIV B   5       8.816   7.319  -6.922  1.00  0.00           C  
HETATM   77  C3  DIV B   5       8.718   6.285  -5.774  1.00  0.00           C  
HETATM   78  H   DIV B   5      10.344   4.399  -3.738  1.00  0.00           H  
HETATM   79  H1  DIV B   5      12.449   6.363  -6.904  1.00  0.00           H  
HETATM   80  H2  DIV B   5       8.927   7.744  -3.763  1.00  0.00           H  
HETATM   81  H3  DIV B   5      10.662   7.701  -3.507  1.00  0.00           H  
HETATM   82  H4  DIV B   5      10.017   8.335  -5.011  1.00  0.00           H  
HETATM   83  H5  DIV B   5       7.893   7.336  -7.503  1.00  0.00           H  
HETATM   84  H6  DIV B   5       8.977   8.329  -6.544  1.00  0.00           H  
HETATM   85  H7  DIV B   5       9.626   7.085  -7.613  1.00  0.00           H  
HETATM   86  H8  DIV B   5       7.847   6.532  -5.165  1.00  0.00           H  
HETATM   87  H9  DIV B   5       8.492   5.309  -6.207  1.00  0.00           H  
TER      88      DIV A   5
CONECT    1    2    7    8
CONECT    2    1    3    5   12
CONECT    3    2    4   13
CONECT    3    4
CONECT    4    3
CONECT    4    3
CONECT    7    1
CONECT   70   58   71   78
CONECT   71   70   72   75   77
CONECT   72   71   73   74
CONECT   72   73
CONECT   73   72
CONECT   73   72
CONECT   78   70
CONECT   74   72   79
CONECT   79   74
CONECT    8    1
CONECT    5    2    6    9   10
CONECT    6    5   11
CONECT    9    5
CONECT   10    5
CONECT   11    6
CONECT   12    2
CONECT   75   71   80   81   82
CONECT   80   75
CONECT   81   75
CONECT   82   75
CONECT   76   77   83   84   85
CONECT   77   71   76   86   87
CONECT   83   76
CONECT   84   76
CONECT   85   76
CONECT   86   77
CONECT   87   77
END

4. Atom Name Verification

DSN atoms in PDB match topology exactly (12 atoms):
C, CA, CB, H1, H2, HA, HB2, HB3, HG, N, O, OG

DIV atoms in PDB match topology exactly (18 atoms):
C, C1, C2, C3, CA, H, H1, H2, H3, H4, H5, H6, H7, H8, H9, N, O, O1

What We’ve Tried

✓ Combined acpype-generated topologies for DSN and DIV (same format as working IVA)
✓ Removed spurious H atom from DSN carbonyl carbon that acpype incorrectly added
✓ Verified MASS declarations for all custom atom types (NT_, CT_, C_, etc.)
✓ Verified atom names match between PDB and topology files (100% match)
✓ Ensured proper file format (set echo, autogenerate, END blocks)
✓ Added DSN+DIV to standard protein-allhdg5-4.top (but HETATM records still get sanitized)
✓ Converted HETATM→ATOM in PDB (helps with sanitization but doesn’t fix topology generation)

Questions

Why does a combined topology file with multiple RESIdue blocks fail when a single RESIdue file works?
- IVA topology has 1 RESIdue: WORKS ✓
- Combined has 2 RESIdue blocks (DSN + DIV): FAILS ✗
Is there a size/complexity limit for ligand topology files?
- Combined file: 224 lines
- IVA file: 144 lines
How can I get actual CNS error output for debugging?
- clean=false doesn’t generate .err or .out files
- Silent failure makes debugging impossible
Is there a recommended approach for handling multiple non-standard residues in one molecule?
- Should they be separate topology files?
- Can ligand_top_fname accept arrays?
- Different approach entirely?

System Info

HADDOCK3 version: v2025.11.0
Python: 3.10.19 | packaged by conda-forge
Topology generator: acpype v2023.10.27
Input source: Maestro-generated PDB files

Any guidance would be greatly appreciated! Happy to provide additional files or debugging information.

amjjbonvin · February 6, 2026, 8:58am

The chirality is automatically detected. So a D-SER should be simply named SER and D will be detected if the structure you provide indeed has a D chirality.

Isovaline is not a standard amino acid and we won’t have support for it.

VGPReys · February 6, 2026, 9:04am

Dear user,

Thanks for that very detailed explanation of your system !

Regarding your question:

Surprising
This can be, but we have increased the memory slots than can handle topology limits in CNS, and this should not be an issue anymore.
debug = true in the general parameters (not clean is simply compressing the outputs)
- you cannot add multiple topology / param files
- multiple topologies in the same file should be functional
- there is no way to add linkages, which is a current limitation

Finally, if you want, you can send me the parameters and topology files for the 2 residues (DIB and IVA), and I can implement them directly into haddock3, so they will be part of the library of known residues and usable by any users, which would be nice for the entire community.

IsovalineDude · February 6, 2026, 9:17am

Dear Professor Bonvin,

Thank you for your prompt response. I think I might have a solution.

I got L- Isovaline to work by importing the topology file that I have attached and has imported in the cfg file.

Would that be an acceptable solution?
Would I be able to use a combined topology file that contains say Isovaline and another unsupported amino acid? Trying to see what my issue is, is it with the formatting of the file or something else.

Thanks & Regards,
AS

IsovalineDude · February 6, 2026, 9:20am

Dear VGPReys,

Thank you so much,

That would be great,

I believe my topology files should be there. Let me get you the param files too.

Thanks & Regards,
AS

IsovalineDude · February 10, 2026, 8:11am

Dear VGPReys, @VGPReys

IVA.params

Remarks IVAminimized_CNS.par created by acpype (v: 2023.10.27) on Tue Feb 10 00:02:27 2026

set echo=false end

{ Bonds: atomType1 atomType2 kb r0 }
BOND   NT_    H_   1000.0   1.0100
BOND   CT_   HC_   1000.0   1.0900
BOND   OH_   HO_   1000.0   0.9600
BOND   NT_   CT_   1000.0   1.4710
BOND   CT_   CT_   1000.0   1.5260
BOND   CT_    C_   1000.0   1.5220
BOND    C_    O_   1000.0   1.2290
BOND    C_   OH_   1000.0   1.3640

{ Angles: aType1 aType2 aType3 kt t0 }
ANGLe   CT_   NT_    H_    500.0   109.50
ANGLe   CT_   CT_   HC_    500.0   109.50
ANGLe    C_   OH_   HO_    500.0   113.00
ANGLe    H_   NT_    H_    500.0   109.50
ANGLe   HC_   CT_   HC_    500.0   109.50
ANGLe   NT_   CT_   CT_    500.0   111.20
ANGLe   NT_   CT_    C_    500.0   113.36
ANGLe   CT_   CT_   CT_    500.0   109.50
ANGLe   CT_    C_    O_    500.0   120.40
ANGLe   CT_    C_   OH_    500.0   110.00
ANGLe   CT_   CT_    C_    500.0   111.10
ANGLe    O_    C_   OH_    500.0   120.00

{ Proper Dihedrals: aType1 aType2 aType3 aType4 kt period phase }
DIHEdral   CT_   CT_   CT_   HC_         750.000    3     0.00
DIHEdral   CT_   CT_    C_    O_  MULT 3 750.000    1     0.00
                                         750.000    2   180.00
                                         750.000    3   180.00
DIHEdral   NT_   CT_    C_   OH_         750.000    0     0.00
DIHEdral    H_   NT_   CT_    C_         750.000    3     0.00
DIHEdral   CT_    C_   OH_   HO_         750.000    2   180.00
DIHEdral   NT_   CT_   CT_   CT_         750.000    3     0.00
DIHEdral   NT_   CT_    C_    O_         750.000    0     0.00
DIHEdral    O_    C_   OH_   HO_  MULT 2 750.000    1     0.00
                                         750.000    2   180.00
DIHEdral   CT_   CT_   CT_    C_  MULT 3 750.000    1   180.00
                                         750.000    2     0.00
                                         750.000    0     0.00
DIHEdral   HC_   CT_   CT_   HC_         750.000    3     0.00
DIHEdral   NT_   CT_   CT_   HC_         750.000    3     0.00
DIHEdral   CT_   CT_    C_   OH_         750.000    0     0.00
DIHEdral    C_   CT_   CT_   HC_         750.000    3     0.00
DIHEdral    H_   NT_   CT_   CT_         750.000    3     0.00
DIHEdral   CT_   CT_   CT_   CT_  MULT 3 750.000    1   180.00
                                         750.000    2   180.00
                                         750.000    3     0.00

{ Improper Dihedrals: aType1 aType2 aType3 aType4 kt period phase }
IMPRoper   CT_    O_    C_   OH_         750.0    2   180.00
IMPRoper   NT_   CT_   CT_    C_       11000.0    0    70.51

{ Nonbonded: Type Emin sigma; (1-4): Emin/2 sigma }
NONBonded   NT_    0.170000    3.249999    0.085000    3.249999
NONBonded   CT_    0.109400    3.399670    0.054700    3.399670
NONBonded    C_    0.086000    3.399670    0.043000    3.399670
NONBonded    O_    0.210000    2.959922    0.105000    2.959922
NONBonded   OH_    0.210400    3.066473    0.105200    3.066473
NONBonded    H_    0.015700    1.069078    0.007850    1.069078
NONBonded   HC_    0.015700    2.649533    0.007850    2.649533
NONBonded   HO_    0.000000    0.000000    0.000000    0.000000

set echo=true end

IVA.top

Remarks IVAminimized_CNS.top created by acpype (v: 2023.10.27) on Tue Feb 10 00:02:27 2026

set echo=false end

autogenerate angles=True dihedrals=True end

{ atomType  mass }
MASS NT_     14.010
MASS CT_     12.010
MASS C_      12.010
MASS O_      16.000
MASS OH_     16.000
MASS H_       1.008
MASS HC_      1.008
MASS HO_      1.008

RESIdue IVA

GROUP

{ atomName  atomType  Charge }
ATOM N     TYPE= NT_   CHARGE=  -0.8988 END
ATOM CA    TYPE= CT_   CHARGE=   0.1522 END
ATOM CB1   TYPE= CT_   CHARGE=  -0.0734 END
ATOM CG1   TYPE= CT_   CHARGE=  -0.0961 END
ATOM CB2   TYPE= CT_   CHARGE=  -0.1361 END
ATOM C     TYPE= C_    CHARGE=   0.6411 END
ATOM O     TYPE= O_    CHARGE=  -0.5440 END
ATOM OXT   TYPE= OH_   CHARGE=  -0.6121 END
ATOM H     TYPE= H_    CHARGE=   0.3638 END
ATOM H2    TYPE= H_    CHARGE=   0.3638 END
ATOM HB11  TYPE= HC_   CHARGE=   0.0642 END
ATOM HB12  TYPE= HC_   CHARGE=   0.0642 END
ATOM HG11  TYPE= HC_   CHARGE=   0.0374 END
ATOM HG12  TYPE= HC_   CHARGE=   0.0374 END
ATOM HG13  TYPE= HC_   CHARGE=   0.0374 END
ATOM HB21  TYPE= HC_   CHARGE=   0.0514 END
ATOM HB22  TYPE= HC_   CHARGE=   0.0514 END
ATOM HB23  TYPE= HC_   CHARGE=   0.0514 END
ATOM HXT   TYPE= HO_   CHARGE=   0.4450 END

{ Bonds: atomName1  atomName2 }
BOND N     H    
BOND N     H2   
BOND CB1   HB11 
BOND CB1   HB12 
BOND CG1   HG11 
BOND CG1   HG12 
BOND CG1   HG13 
BOND CB2   HB21 
BOND CB2   HB22 
BOND CB2   HB23 
BOND OXT   HXT  
BOND N     CA   
BOND CA    CB1  
BOND CA    CB2  
BOND CA    C    
BOND CB1   CG1  
BOND C     O    
BOND C     OXT  

{ Angles: atomName1 atomName2 atomName3}
ANGLe CA    N     H    
ANGLe CA    N     H2   
ANGLe CA    CB1   HB11 
ANGLe CA    CB1   HB12 
ANGLe CA    CB2   HB21 
ANGLe CA    CB2   HB22 
ANGLe CA    CB2   HB23 
ANGLe CB1   CG1   HG11 
ANGLe CB1   CG1   HG12 
ANGLe CB1   CG1   HG13 
ANGLe CG1   CB1   HB11 
ANGLe CG1   CB1   HB12 
ANGLe C     OXT   HXT  
ANGLe H     N     H2   
ANGLe HB11  CB1   HB12 
ANGLe HG11  CG1   HG12 
ANGLe HG11  CG1   HG13 
ANGLe HG12  CG1   HG13 
ANGLe HB21  CB2   HB22 
ANGLe HB21  CB2   HB23 
ANGLe HB22  CB2   HB23 
ANGLe N     CA    CB1  
ANGLe N     CA    CB2  
ANGLe N     CA    C    
ANGLe CA    CB1   CG1  
ANGLe CA    C     O    
ANGLe CA    C     OXT  
ANGLe CB1   CA    CB2  
ANGLe CB1   CA    C    
ANGLe CB2   CA    C    
ANGLe O     C     OXT  

{ Proper Dihedrals: name1 name2 name3 name4 }
DIHEdral N     CA    CB1   HB11 
DIHEdral N     CA    CB1   HB12 
DIHEdral N     CA    CB2   HB21 
DIHEdral N     CA    CB2   HB22 
DIHEdral N     CA    CB2   HB23 
DIHEdral CA    CB1   CG1   HG11 
DIHEdral CA    CB1   CG1   HG12 
DIHEdral CA    CB1   CG1   HG13 
DIHEdral CA    C     OXT   HXT  
DIHEdral H     N     CA    CB1  
DIHEdral H2    N     CA    CB1  
DIHEdral CB1   CA    CB2   HB21 
DIHEdral CB1   CA    CB2   HB22 
DIHEdral CB1   CA    CB2   HB23 
DIHEdral H     N     CA    CB2  
DIHEdral H2    N     CA    CB2  
DIHEdral CB2   CA    CB1   HB11 
DIHEdral CB2   CA    CB1   HB12 
DIHEdral H     N     CA    C    
DIHEdral H2    N     CA    C    
DIHEdral C     CA    CB1   HB11 
DIHEdral C     CA    CB1   HB12 
DIHEdral C     CA    CB2   HB21 
DIHEdral C     CA    CB2   HB22 
DIHEdral C     CA    CB2   HB23 
DIHEdral O     C     OXT   HXT  
DIHEdral HB11  CB1   CG1   HG11 
DIHEdral HB11  CB1   CG1   HG12 
DIHEdral HB11  CB1   CG1   HG13 
DIHEdral HB12  CB1   CG1   HG11 
DIHEdral HB12  CB1   CG1   HG12 
DIHEdral HB12  CB1   CG1   HG13 
DIHEdral N     CA    CB1   CG1  
DIHEdral N     CA    C     O    
DIHEdral N     CA    C     OXT  
DIHEdral CB1   CA    C     O    
DIHEdral CB1   CA    C     OXT  
DIHEdral CG1   CB1   CA    CB2  
DIHEdral CG1   CB1   CA    C    
DIHEdral CB2   CA    C     O    
DIHEdral CB2   CA    C     OXT  

{ Improper Dihedrals: aName1 aName2 aName3 aName4 }
IMPRoper CA    O     C     OXT  
IMPRoper N     CB1   CB2   C    

END {RESIdue IVA}

set echo=true end

Howver now when I try to do flex-ref I can see that jsut the isovaline is about 100 angstroms away. Kinda stuck on what to do from here.

Heres the PDB of the IVA

TITLE     IVA
REMARK   4      COMPLIES WITH FORMAT V. 3.0, 1-DEC-2006
REMARK 888
REMARK 888 WRITTEN BY MAESTRO (A PRODUCT OF SCHRODINGER, LLC)
COMPND    IVA_Minimized.pdb 
AUTHOR    GENERATED BY OPEN BABEL 2.4.1
HETATM    1  N   IVA     0       0.344   1.209  -0.984  1.00  0.00           N  
HETATM    2  CA  IVA     0       0.132   0.217   0.060  1.00  0.00           C  
HETATM    3  CB1 IVA     0       0.860  -1.075  -0.418  1.00  0.00           C  
HETATM    4  CG1 IVA     0       2.385  -0.985  -0.671  1.00  0.00           C  
HETATM    5  CB2 IVA     0       0.780   0.804   1.330  1.00  0.00           C  
HETATM    6  C   IVA     0      -1.416  -0.025   0.242  1.00  0.00           C  
HETATM    7  O   IVA     0      -1.991  -1.077  -0.037  1.00  0.00           O  
HETATM    8  OXT IVA     0      -2.083   1.047   0.751  1.00  0.00           O  
HETATM    9  H   IVA     0       0.624   2.072  -0.536  1.00  0.00           H  
HETATM   10  H2  IVA     0       1.149   0.911  -1.519  1.00  0.00           H  
HETATM   11 HB11 IVA     0       0.385  -1.439  -1.332  1.00  0.00           H  
HETATM   12 HB12 IVA     0       0.690  -1.862   0.318  1.00  0.00           H  
HETATM   13 HG11 IVA     0       2.636  -0.239  -1.426  1.00  0.00           H  
HETATM   14 HG12 IVA     0       2.934  -0.739   0.238  1.00  0.00           H  
HETATM   15 HG13 IVA     0       2.772  -1.941  -1.026  1.00  0.00           H  
HETATM   16 HB21 IVA     0       1.830   1.057   1.185  1.00  0.00           H  
HETATM   17 HB22 IVA     0       0.279   1.714   1.666  1.00  0.00           H  
HETATM   18 HB23 IVA     0       0.733   0.091   2.154  1.00  0.00           H  
HETATM   19  HXT IVA     0      -3.007   0.794   0.798  1.00  0.00           H  
CONECT    1    2    9   10                                            
CONECT    2    1    3    5    6                                       
CONECT    3    2    4   11   12                                       
CONECT    4    3   13   14   15                                       
CONECT    5    2   16   17   18                                       
CONECT    6    2    7    8                                            
CONECT    7    6                                                      
CONECT    8    6   19                                                 
CONECT    9    1                                                      
CONECT   10    1                                                      
CONECT   11    3                                                      
CONECT   12    3                                                      
CONECT   13    4                                                      
CONECT   14    4                                                      
CONECT   15    4                                                      
CONECT   16    5                                                      
CONECT   17    5                                                      
CONECT   18    5                                                      
CONECT   19    8                                                      
MASTER        0    0    0    0    0    0    0    0   19    0   19    0
END

and the peptide sequence that I am docking

ATOM      1  N   SER B   1       0.535   3.001   5.091  1.00  0.00           N  
ATOM      2  CA  SER B   1       1.263   1.922   5.828  1.00  0.00           C  
ATOM      3  C   SER B   1       2.572   1.475   5.100  1.00  0.00           C  
ATOM      4  O   SER B   1       3.384   0.752   5.685  1.00  0.00           O  
ATOM      5  CB  SER B   1       1.504   2.303   7.314  1.00  0.00           C  
ATOM      6  OG  SER B   1       2.349   3.437   7.458  1.00  0.00           O  
ATOM      9  HA  SER B   1       0.643   1.024   5.833  1.00  0.00           H  
ATOM     11  HB2 SER B   1       0.553   2.510   7.807  1.00  0.00           H  
ATOM     10  HB3 SER B   1       1.947   1.467   7.859  1.00  0.00           H  
ATOM     12  HG  SER B   1       3.248   3.161   7.241  1.00  0.00           H  
ATOM      7  H1  SER B   1      -0.457   2.960   5.300  1.00  0.00           H  
ATOM      8  H2  SER B   1       0.821   3.887   5.501  1.00  0.00           H  
ATOM     13  N   TRP B   2       2.748   1.890   3.842  1.00  0.00           N  
ATOM     14  CA  TRP B   2       3.903   1.620   2.997  1.00  0.00           C  
ATOM     15  C   TRP B   2       4.007   2.740   1.957  1.00  0.00           C  
ATOM     16  O   TRP B   2       2.985   3.305   1.564  1.00  0.00           O  
ATOM     17  CB  TRP B   2       3.766   0.223   2.346  1.00  0.00           C  
ATOM     18  CG  TRP B   2       4.836  -0.171   1.369  1.00  0.00           C  
ATOM     19  CD1 TRP B   2       5.999  -0.787   1.681  1.00  0.00           C  
ATOM     20  CD2 TRP B   2       4.905   0.115  -0.063  1.00  0.00           C  
ATOM     22  CE2 TRP B   2       6.143  -0.386  -0.565  1.00  0.00           C  
ATOM     23  CE3 TRP B   2       4.052   0.762  -0.988  1.00  0.00           C  
ATOM     21  NE1 TRP B   2       6.764  -0.922   0.541  1.00  0.00           N  
ATOM     24  CZ2 TRP B   2       6.507  -0.269  -1.916  1.00  0.00           C  
ATOM     25  CZ3 TRP B   2       4.414   0.902  -2.344  1.00  0.00           C  
ATOM     26  CH2 TRP B   2       5.638   0.383  -2.809  1.00  0.00           C  
ATOM     27  H   TRP B   2       2.047   2.520   3.464  1.00  0.00           H  
ATOM     28  HA  TRP B   2       4.804   1.646   3.614  1.00  0.00           H  
ATOM     30  HB2 TRP B   2       3.720  -0.542   3.123  1.00  0.00           H  
ATOM     29  HB3 TRP B   2       2.814   0.166   1.815  1.00  0.00           H  
ATOM     31  HD1 TRP B   2       6.273  -1.111   2.677  1.00  0.00           H  
ATOM     32  HE1 TRP B   2       7.681  -1.353   0.550  1.00  0.00           H  
ATOM     33  HE3 TRP B   2       3.110   1.166  -0.645  1.00  0.00           H  
ATOM     34  HZ2 TRP B   2       7.455  -0.658  -2.261  1.00  0.00           H  
ATOM     35  HZ3 TRP B   2       3.747   1.407  -3.029  1.00  0.00           H  
ATOM     36  HH2 TRP B   2       5.912   0.490  -3.849  1.00  0.00           H  
ATOM     37  N   LEU B   3       5.232   2.997   1.497  1.00  0.00           N  
ATOM     38  CA  LEU B   3       5.560   3.853   0.367  1.00  0.00           C  
ATOM     39  C   LEU B   3       6.968   3.451  -0.087  1.00  0.00           C  
ATOM     40  O   LEU B   3       7.736   2.903   0.706  1.00  0.00           O  
ATOM     41  CB  LEU B   3       5.456   5.346   0.781  1.00  0.00           C  
ATOM     42  CG  LEU B   3       5.744   6.395  -0.323  1.00  0.00           C  
ATOM     43  CD1 LEU B   3       4.828   6.227  -1.556  1.00  0.00           C  
ATOM     44  CD2 LEU B   3       5.687   7.826   0.253  1.00  0.00           C  
ATOM     45  H   LEU B   3       6.025   2.451   1.814  1.00  0.00           H  
ATOM     46  HA  LEU B   3       4.860   3.628  -0.440  1.00  0.00           H  
ATOM     48  HB2 LEU B   3       4.456   5.535   1.175  1.00  0.00           H  
ATOM     47  HB3 LEU B   3       6.138   5.517   1.616  1.00  0.00           H  
ATOM     49  HG  LEU B   3       6.773   6.261  -0.660  1.00  0.00           H  
ATOM     50 HD11 LEU B   3       4.410   7.172  -1.903  1.00  0.00           H  
ATOM     51 HD12 LEU B   3       5.380   5.808  -2.398  1.00  0.00           H  
ATOM     52 HD13 LEU B   3       3.983   5.567  -1.357  1.00  0.00           H  
ATOM     53 HD21 LEU B   3       6.599   8.376   0.018  1.00  0.00           H  
ATOM     54 HD22 LEU B   3       4.851   8.408  -0.136  1.00  0.00           H  
ATOM     55 HD23 LEU B   3       5.587   7.828   1.339  1.00  0.00           H  
ATOM     56  N   THR B   4       7.293   3.744  -1.344  1.00  0.00           N  
ATOM     57  CA  THR B   4       8.618   3.680  -1.939  1.00  0.00           C  
ATOM     58  C   THR B   4       8.526   4.572  -3.187  1.00  0.00           C  
ATOM     59  O   THR B   4       7.449   4.652  -3.783  1.00  0.00           O  
ATOM     60  CB  THR B   4       8.996   2.226  -2.337  1.00  0.00           C  
ATOM     62  CG2 THR B   4      10.208   2.058  -3.270  1.00  0.00           C  
ATOM     61  OG1 THR B   4       9.297   1.502  -1.159  1.00  0.00           O  
ATOM     63  H   THR B   4       6.617   4.161  -1.974  1.00  0.00           H  
ATOM     64  HA  THR B   4       9.350   4.097  -1.244  1.00  0.00           H  
ATOM     65  HB  THR B   4       8.138   1.758  -2.820  1.00  0.00           H  
ATOM     66  HG1 THR B   4       8.656   1.761  -0.474  1.00  0.00           H  
ATOM     67 HG21 THR B   4      10.451   1.004  -3.406  1.00  0.00           H  
ATOM     68 HG22 THR B   4      10.018   2.466  -4.263  1.00  0.00           H  
ATOM     69 HG23 THR B   4      11.094   2.550  -2.868  1.00  0.00           H  
HETATM   71  N   IVA B   5       9.635   5.253  -3.520  1.00  0.00           N  
HETATM   72  CA  IVA B   5       9.820   6.235  -4.613  1.00  0.00           C  
HETATM   73  C   IVA B   5       9.480   5.573  -6.017  1.00  0.00           C  
HETATM   74  O   IVA B   5       8.563   6.041  -6.732  1.00  0.00           O  
HETATM   76  C1  IVA B   5      11.328   6.610  -4.592  1.00  0.00           C  
HETATM   75  O1  IVA B   5      10.148   4.574  -6.382  1.00  0.00           O1-
HETATM   77  C2  IVA B   5       9.243   8.787  -5.117  1.00  0.00           C  
HETATM   78  C3  IVA B   5       8.960   7.512  -4.291  1.00  0.00           C  
HETATM   79  HN  IVA B   5      10.423   5.171  -2.896  1.00  0.00           H  
HETATM   80  H1  IVA B   5      11.594   7.271  -5.417  1.00  0.00           H  
HETATM   81  H2  IVA B   5      11.598   7.124  -3.669  1.00  0.00           H  
HETATM   82  H3  IVA B   5      11.974   5.733  -4.668  1.00  0.00           H  
HETATM   83  H4  IVA B   5       8.549   9.582  -4.842  1.00  0.00           H  
HETATM   84  H5  IVA B   5      10.249   9.167  -4.940  1.00  0.00           H  
HETATM   85  H6  IVA B   5       9.133   8.619  -6.188  1.00  0.00           H  
HETATM   86  H7  IVA B   5       9.101   7.776  -3.241  1.00  0.00           H  
HETATM   87  H8  IVA B   5       7.898   7.272  -4.372  1.00  0.00           H  
TER   
CONECT   58   71
CONECT   71   58   72   79
CONECT   72   71   73   76   78
CONECT   73   72   74   75
CONECT   74   73
CONECT   75   73
CONECT   76   72   80   81   82
CONECT   77   78   83   84   85
CONECT   78   72   77   86   87
CONECT   79   71
CONECT   80   76
CONECT   81   76
CONECT   82   76
CONECT   83   77
CONECT   84   77
CONECT   85   77
CONECT   86   78
CONECT   87   78
END

Would really appreciate some help!

Thanks and regards

AS

amjjbonvin · February 10, 2026, 9:18am

The only way to get it incorporated properly in your peptide, with peptide bonds added, is to match the naming of the IVA atom types to that of regular amino acids. You will most likely have to add a few missing parameters.

For this process, you would need a test peptide with IVA in the middle.

Now your IVA moves away because the peptide bonds are not detected.

And for consistency with the other amino acids, I would also try to match the partial charges to those of similar amino acids (e.g. VAL)

VGPReys · February 11, 2026, 11:58am

I will try to address this asap within a HADDOCK3 pull-request to implement it directly in the code / force-field.

IsovalineDude · February 12, 2026, 7:35am

Dear Dr. Reys,

Thanks so much. I have generated the top/par and am currently working on testing it.

Will submit a Pull Req for your kind review later this week.

Thanks & Regards
AS

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