Pmx ligandHybrid list index out of range error

pmx
1

Hello,

I am currently using pmx to create hybrid topologies and ran into an list index error:
IndexError: list index out of range

I used ligandHybrid from pmx:
pmx ligandHybrid -i1 t1.pdb -i2 t2.pdb -itp1 t1.itp -itp2 t2.itp -pairs pairs2.dat

It was recommended from the other topics to swap the inputs, which resulted in the same list index error:

pmx ligandHybrid -i1 t2.pdb -i2 t1.pdb -itp1 t2.itp -itp2 t1.itp -pairs pairs2.dat

The itp files look like this:
t1:

; Created by cgenff_charmm2gmx.py

[ moleculetype ]
; Name			   nrexcl
SAMPLmol.pdb				 3

[ atoms ]
;	 nr		  type	resnr residue  atom   cgnr	   charge		mass  typeB    chargeB		massB
; residue	 1 SAMPLmol.pdb rtp SAMPLmol.pdb q	qsum
     1      OG311      1 SAMPLmol.pdb     O1      1     -0.537     15.999   ;
     2     CG2R61      1 SAMPLmol.pdb     C1      2      0.419     12.011   ;
     3     CG2R61      1 SAMPLmol.pdb     C2      3     -0.120     12.011   ;
     4     CG2R61      1 SAMPLmol.pdb     C3      4     -0.107     12.011   ;
     5     CG2R61      1 SAMPLmol.pdb     C4      5     -0.009     12.011   ;
     6     CG2R61      1 SAMPLmol.pdb     C5      6     -0.114     12.011   ;
     7     CG2R61      1 SAMPLmol.pdb     C6      7     -0.110     12.011   ;
     8     CG2R61      1 SAMPLmol.pdb     C7      8     -0.104     12.011   ;
     9     CG2R61      1 SAMPLmol.pdb     C8      9     -0.132     12.011   ;
    10     CG2R61      1 SAMPLmol.pdb     C9     10      0.294     12.011   ;
    11     NG2R60      1 SAMPLmol.pdb     N1     11     -0.590     14.007   ;
    12       HGP1      1 SAMPLmol.pdb     H1     12      0.420      1.008   ;
    13      HGR61      1 SAMPLmol.pdb     H2     13      0.115      1.008   ;
    14      HGR61      1 SAMPLmol.pdb     H3     14      0.115      1.008   ;
    15      HGR61      1 SAMPLmol.pdb     H4     15      0.115      1.008   ;
    16      HGR61      1 SAMPLmol.pdb     H5     16      0.115      1.008   ;
    17      HGR61      1 SAMPLmol.pdb     H6     17      0.115      1.008   ;
    18      HGR61      1 SAMPLmol.pdb     H7     18      0.115      1.008   ;

[ bonds ]
;	ai	  aj funct			  c0			c1			  c2			c3
    1     2	 1
    1    12	 1
    2     3	 1
    2    11	 1
    3     4	 1
    3    13	 1
    4     5	 1
    4    14	 1
    5    10	 1
    5     6	 1
    6    15	 1
    6     7	 1
    7    16	 1
    7     8	 1
    8     9	 1
    8    17	 1
    9    10	 1
    9    18	 1
   10    11	 1

[ pairs ]
;	ai	  aj funct			  c0			c1			  c2			c3
    1    10	 1
    1     4	 1
    1    13	 1
    2     9	 1
    2     5	 1
    2    14	 1
    3    10	 1
    3    12	 1
    3     6	 1
    4     9	 1
    4    11	 1
    4     7	 1
    4    15	 1
    5     8	 1
    5    13	 1
    5    18	 1
    5    16	 1
    6     9	 1
    6    17	 1
    6    11	 1
    6    14	 1
    7    10	 1
    7    18	 1
    8    11	 1
    8    15	 1
    9    16	 1
   10    14	 1
   10    15	 1
   10    17	 1
   11    12	 1
   11    13	 1
   11    18	 1
   13    14	 1
   15    16	 1
   16    17	 1
   17    18	 1

[ angles ]
;	ai	  aj	ak funct			c0			  c1			c2			  c3
    2     1    12	5
    1     2     3	5
    1     2    11	5
    3     2    11	5
    2     3     4	5
    2     3    13	5
    4     3    13	5
    3     4     5	5
    3     4    14	5
    5     4    14	5
   10     5     4	5
   10     5     6	5
    4     5     6	5
    5     6    15	5
    5     6     7	5
   15     6     7	5
   16     7     6	5
   16     7     8	5
    6     7     8	5
    9     8    17	5
    9     8     7	5
   17     8     7	5
   10     9    18	5
   10     9     8	5
   18     9     8	5
    9    10    11	5
    9    10     5	5
   11    10     5	5
    2    11    10	5

[ dihedrals ]
;	ai	  aj	ak	  al funct			  c0			c1			  c2			c3			  c4			c5
   12     1     2     3	 9
   12     1     2    11	 9
    1     2     3     4	 9
    1     2     3    13	 9
   11     2     3     4	 9
   11     2     3    13	 9
    1     2    11    10	 9
    3     2    11    10	 9
    2     3     4     5	 9
    2     3     4    14	 9
   13     3     4     5	 9
   13     3     4    14	 9
    3     4     5    10	 9
    3     4     5     6	 9
   14     4     5    10	 9
   14     4     5     6	 9
    4     5    10     9	 9
    4     5    10    11	 9
    6     5    10     9	 9
    6     5    10    11	 9
   10     5     6    15	 9
   10     5     6     7	 9
    4     5     6    15	 9
    4     5     6     7	 9
    5     6     7    16	 9
    5     6     7     8	 9
   15     6     7    16	 9
   15     6     7     8	 9
   16     7     8     9	 9
   16     7     8    17	 9
    6     7     8     9	 9
    6     7     8    17	 9
   17     8     9    10	 9
   17     8     9    18	 9
    7     8     9    10	 9
    7     8     9    18	 9
   18     9    10    11	 9
   18     9    10     5	 9
    8     9    10    11	 9
    8     9    10     5	 9
    9    10    11     2	 9
    5    10    11     2	 9

t2:

; Created by cgenff_charmm2gmx.py

[ moleculetype ]
; Name			   nrexcl
SAMPLmol.pdb				 3

[ atoms ]
;	 nr		  type	resnr residue  atom   cgnr	   charge		mass  typeB    chargeB		massB
; residue	 1 SAMPLmol.pdb rtp SAMPLmol.pdb q	qsum
     1      OG2D4      1 SAMPLmol.pdb     O1      1     -0.470     15.999   ;
     2     CG2R63      1 SAMPLmol.pdb     C1      2      0.183     12.011   ;
     3     NG2R61      1 SAMPLmol.pdb     N1      3     -0.286     14.007   ;
     4     CG2R62      1 SAMPLmol.pdb     C2      4      0.286     12.011   ;
     5     CG2R62      1 SAMPLmol.pdb     C3      5     -0.086     12.011   ;
     6     CG2R61      1 SAMPLmol.pdb     C4      6     -0.108     12.011   ;
     7     CG2R61      1 SAMPLmol.pdb     C5      7     -0.112     12.011   ;
     8     CG2R61      1 SAMPLmol.pdb     C6      8     -0.111     12.011   ;
     9     CG2R61      1 SAMPLmol.pdb     C7      9     -0.108     12.011   ;
    10     CG2R62      1 SAMPLmol.pdb     C8     10     -0.196     12.011   ;
    11     CG2R62      1 SAMPLmol.pdb     C9     11     -0.173     12.011   ;
    12       HGP1      1 SAMPLmol.pdb     H1     12      0.300      1.008   ;
    13      HGR61      1 SAMPLmol.pdb     H2     13      0.115      1.008   ;
    14      HGR61      1 SAMPLmol.pdb     H3     14      0.115      1.008   ;
    15      HGR61      1 SAMPLmol.pdb     H4     15      0.115      1.008   ;
    16      HGR61      1 SAMPLmol.pdb     H5     16      0.115      1.008   ;
    17      HGR62      1 SAMPLmol.pdb     H6     17      0.226      1.008   ;
    18      HGR62      1 SAMPLmol.pdb     H7     18      0.195      1.008   ;

[ bonds ]
;	ai	  aj funct			  c0			c1			  c2			c3
    1     2	 1
    2     3	 1
    2    11	 1
    3    12	 1
    3     4	 1
    4     9	 1
    4     5	 1
    5    10	 1
    5     6	 1
    6    13	 1
    6     7	 1
    7    14	 1
    7     8	 1
    8     9	 1
    8    15	 1
    9    16	 1
   10    17	 1
   10    11	 1
   11    18	 1

[ pairs ]
;	ai	  aj funct			  c0			c1			  c2			c3
    1     4	 1
    1    18	 1
    1    12	 1
    1    10	 1
    2     9	 1
    2    17	 1
    2     5	 1
    3     8	 1
    3    18	 1
    3    16	 1
    3     6	 1
    3    10	 1
    4     7	 1
    4    11	 1
    4    13	 1
    4    15	 1
    4    17	 1
    5     8	 1
    5    12	 1
    5    14	 1
    5    16	 1
    5    18	 1
    6     9	 1
    6    17	 1
    6    11	 1
    6    15	 1
    7    10	 1
    7    16	 1
    8    13	 1
    9    12	 1
    9    14	 1
    9    10	 1
   10    13	 1
   11    12	 1
   13    14	 1
   14    15	 1
   15    16	 1
   17    18	 1

[ angles ]
;	ai	  aj	ak funct			c0			  c1			c2			  c3
    1     2     3	5
    1     2    11	5
    3     2    11	5
   12     3     2	5
   12     3     4	5
    2     3     4	5
    9     4     3	5
    9     4     5	5
    3     4     5	5
   10     5     4	5
   10     5     6	5
    4     5     6	5
   13     6     5	5
   13     6     7	5
    5     6     7	5
   14     7     6	5
   14     7     8	5
    6     7     8	5
    9     8    15	5
    9     8     7	5
   15     8     7	5
   16     9     4	5
   16     9     8	5
    4     9     8	5
   17    10    11	5
   17    10     5	5
   11    10     5	5
    2    11    18	5
    2    11    10	5
   18    11    10	5

[ dihedrals ]
;	ai	  aj	ak	  al funct			  c0			c1			  c2			c3			  c4			c5
    1     2     3    12	 9
    1     2     3     4	 9
   11     2     3    12	 9
   11     2     3     4	 9
    1     2    11    18	 9
    1     2    11    10	 9
    3     2    11    18	 9
    3     2    11    10	 9
   12     3     4     9	 9
   12     3     4     5	 9
    2     3     4     9	 9
    2     3     4     5	 9
    3     4     9    16	 9
    3     4     9     8	 9
    5     4     9    16	 9
    5     4     9     8	 9
    9     4     5    10	 9
    9     4     5     6	 9
    3     4     5    10	 9
    3     4     5     6	 9
    4     5    10    17	 9
    4     5    10    11	 9
    6     5    10    17	 9
    6     5    10    11	 9
   10     5     6    13	 9
   10     5     6     7	 9
    4     5     6    13	 9
    4     5     6     7	 9
   13     6     7    14	 9
   13     6     7     8	 9
    5     6     7    14	 9
    5     6     7     8	 9
   14     7     8     9	 9
   14     7     8    15	 9
    6     7     8     9	 9
    6     7     8    15	 9
   15     8     9    16	 9
   15     8     9     4	 9
    7     8     9    16	 9
    7     8     9     4	 9
   17    10    11     2	 9
   17    10    11    18	 9
    5    10    11     2	 9
    5    10    11    18	 9

[ dihedrals ]
;	ai	  aj	ak	  al funct			  c0			c1			  c2			c3
    2    11     3     1	 2
2

Hello,

Could you please share the pdb files (t2.pdb, t1.pdb) and the screenshot of the error? It will help me to reproduce and resolve the same.

Thanks,
Sudarshan

3

Hello,

here are the requested files:

t1.pdb:

HEADER    PROTEIN                                 06-JUL-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-JUL-23         0                                  
HETATM    1  O   UNK     0       0.000  -3.080   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0       2.667  -3.080   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3   11                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   10                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9    5   11                                                  
CONECT   11   10    2                                                       
MASTER        0    0    0    0    0    0    0    0   11    0   24    0
END

t2.pdb:

HEADER    PROTEIN                                 06-JUL-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-JUL-23         0                                  
HETATM    1  O   UNK     0      -2.667  -3.080   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       0.000  -3.080   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.000  -0.000   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   11                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    9                                                  
CONECT    5    4    6   10                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8    4                                                       
CONECT   10    5   11                                                       
CONECT   11   10    2                                                       
MASTER        0    0    0    0    0    0    0    0   11    0   24    0
END

The error:

ligandHybridTop__log_> Reading ligand 1 from: "t1.pdb"
ligandHybridTop__log_> Reading ligand 2 from: "t2.pdb"
ligandHybridTop__log_> Reading topology 1 from: "t1.itp"
ligandHybridTop__log_> Reading topology 2 from: "t2.itp"
ligandHybridTop__log_> Reading file with atom pairs: "pairs2.dat"
ligandHybridTop__log_> Assigning forcefield parameters....
ligandHybridTop__log_> Superimposing mol2 on mol1
ligandHybridTop__log_> Superimposing mol1 on mol2
ligandHybridTop__log_> Initializing the main object for LigandHybridTopology
ligandHybridTop__log_> Starting hybrid topology generation
ligandHybridTop__log_> Making atom pairs.....
ligandHybridTop__log_> Identifying dummies.....
ligandHybridTop__log_> Generated 11 atom-atom pairs
ligandHybridTop__log_> Dummies in state A: 0
ligandHybridTop__log_> Dummies in state B: 0
ligandHybridTop__log_> Making B-states....
ligandHybridTop__log_> Atom....:    1         OG311 |  -0.54 |  16.00 ->        OG2D4 |  -0.47 |  16.00
ligandHybridTop__log_> Atom....:    2        CG2R61 |   0.42 |  12.01 ->       CG2R63 |   0.18 |  12.01
ligandHybridTop__log_> Atom....:   11        NG2R60 |  -0.59 |  14.01 ->       NG2R61 |  -0.29 |  14.01
ligandHybridTop__log_> Atom....:   10        CG2R61 |   0.29 |  12.01 ->       CG2R62 |   0.29 |  12.01
ligandHybridTop__log_> Atom....:    5        CG2R61 |  -0.01 |  12.01 ->       CG2R62 |  -0.09 |  12.01
ligandHybridTop__log_> Atom....:    6        CG2R61 |  -0.11 |  12.01 ->       CG2R61 |  -0.11 |  12.01
ligandHybridTop__log_> Atom....:    7        CG2R61 |  -0.11 |  12.01 ->       CG2R61 |  -0.11 |  12.01
ligandHybridTop__log_> Atom....:    8        CG2R61 |  -0.10 |  12.01 ->       CG2R61 |  -0.11 |  12.01
ligandHybridTop__log_> Atom....:    9        CG2R61 |  -0.13 |  12.01 ->       CG2R61 |  -0.11 |  12.01
ligandHybridTop__log_> Atom....:    4        CG2R61 |  -0.11 |  12.01 ->       CG2R62 |  -0.20 |  12.01
ligandHybridTop__log_> Atom....:    3        CG2R61 |  -0.12 |  12.01 ->       CG2R62 |  -0.17 |  12.01
ligandHybridTop__log_> Constructing dummies....
ligandHybridTop__log_> Dummies in stateA: 
ligandHybridTop__log_> Dummies in stateB: 
ligandHybridTop__log_> Construct bonds....
Traceback (most recent call last):
  File "/bin/pmx", line 33, in <module>
    sys.exit(load_entry_point('pmx==0+untagged.880.g7418dab', 'console_scripts', 'pmx')())
  File "/pmx/scripts/cli.py", line 97, in entry_point
    PmxCli()
  File "/pmx/scripts/cli.py", line 44, in __init__
    getattr(self, args.command)()
  File "/pmx/scripts/cli.py", line 64, in ligandHybrid
    ligandHybrid.entry_point()
  File "/pmx/scripts/ligandHybrid.py", line 189, in entry_point
    main(args)
  File "/pmx/scripts/ligandHybrid.py", line 308, in main
    hybridTop._makeHybridTop( )
  File "/pmx/ligand_alchemy.py", line 2116, in _makeHybridTop
    self._make_bonds()
  File "/lib/python3.10/site-packages/pmx/ligand_alchemy.py", line 2330, in _make_bonds
    entr = self._get_ff_entry([idB1, idB2], self.itp2, what= 'bond')
  File "/lib/python3.10/site-packages/pmx/ligand_alchemy.py", line 2871, in _get_ff_entry
    return(out[3:][0])
IndexError: list index out of range

Best regards,

Limmski

5

Sorry there, had not seen the previous texts, the itp file needs epsilon and sigma values.
https://ask.bioexcel.eu/t/make-hybrid-py-list-index-out-of-range-error/2488/2?u=s.pallav

Regards,
Pallav.

6

The itp files need to have the parameters explicitly defined, i.e. bonds, angles and dihedrals need their parameters in the itp files