[gmx-users] topolbuild ( Failing to read oxygen in H2O )

[大木啓輔]

Dear gromacs users

I have a question why topolbuild fails to read oxygen in H2O.

I want to make a topology file of methane hydrate structure with topolbuild and run simulation in gromacs.

I used following command line:

./topolbuild -n ../HYDRATE_A -dir ../dat/gromacs -ff oplsaa -purge 0

.mol2 file that I  used then { 

@<TRIPOS>MOLECULE
ch4h2o_4.pdb
46 36 10 0 0
SMALL
USER_CHARGES


@<TRIPOS>ATOM
      1 C           5.6060    1.6670    5.1720 C.3       1 LIG1   -0.4588
      2 H           6.2390    2.2990    5.8040 H         1 LIG1    0.1147
      3 H           4.9740    1.0350    5.8040 H         1 LIG1    0.1147
      4 H           4.9740    2.2990    4.5400 H         1 LIG1    0.1147
      5 H           6.2390    1.0350    4.5400 H         1 LIG1    0.1147
        :
     41 O           7.0060    1.7150    8.9340 O.3       9 H2O    -1.1794
     42 H           6.0130    1.7150    9.0510 H         9 H2O     0.5897
     43 H           7.4440    1.7150    9.8330 H         9 H2O     0.5897
     44 O           6.9570    1.7200    1.4090 O.3      10 H2O    -1.1794
     45 H           7.2050    0.8780    1.8880 H        10 H2O     0.5897
     46 H           7.2400    2.5080    1.9570 H        10 H2O     0.5897
@<TRIPOS>BOND
     1    1    2 1
     2    1    3 1
     3    1    4 1
     4    1    5 1
     :
    33   41   42 1
    34   41   43 1
    35   44   45 1
    36   44   46 1
@<TRIPOS>SUBSTRUCTURE
     1 LIG1     1 RESIDUE           4 A     LIG1     0 ROOT
     2 LIG1     6 RESIDUE           4 A     LIG1     0 ROOT
     3 LIG1    11 RESIDUE           4 A     LIG1     0 ROOT
     4 LIG1    16 RESIDUE           4 A     LIG1     0 ROOT
     5 LIG1    21 RESIDUE           4 A     LIG1     0 ROOT
     6 LIG1    26 RESIDUE           4 A     LIG1     0 ROOT
     7 LIG1    31 RESIDUE           4 A     LIG1     0 ROOT
     8 LIG1    36 RESIDUE           4 A     LIG1     0 ROOT
     9 H2O    41 RESIDUE           4 A     H2O     0 ROOT
    10 H2O    44 RESIDUE           4 A     H2O     0 ROOT

}

( this file was used for trial, so this is not hydrate structure )

Then, I got this topology file {
 
; The force field files to be included
#include "ffHYDRATE_A.itp"

 [ moleculetype ]
; name  nrexcl
ch4h2o_4.pdb   3

 [ atoms ]
;  nr    type   resnr   residu   atom   cgnr    charge      mass
    1    opls_138     1       LIG       C    1  -0.45880  12.01100       ;  -0.4588000
    2    opls_140     1       LIG       H    1   0.11470   1.00800       ;  -0.3441000
    3    opls_140     1       LIG       H    1   0.11470   1.00800       ;  -0.2294000
    4    opls_140     1       LIG       H    1   0.11470   1.00800       ;  -0.1147000
    5    opls_140     1       LIG       H    1   0.11470   1.00800       ;   0.0000000
    :
   41         O??     9       H2O       O    9  -1.17940  15.99940       ;  -1.1794000
   42    opls_435     9       H2O       H   10   0.58970   1.00800       ;  -0.5897000
   43    opls_435     9       H2O       H   11   0.58970   1.00800       ;   0.0000000
   44         O??    10       H2O       O   12  -1.17940  15.99940       ;  -1.1794000
   45    opls_435    10       H2O       H   13   0.58970   1.00800       ;  -0.5897000
   46    opls_435    10       H2O       H   14   0.58970   1.00800       ;   0.0000000
; total molecule charge =   0.0000000

 [ bonds ]
;   ai  aj   funct      b0          kb
       1     2   1     0.10900      284512.       ;     C-     H
       1     3   1     0.10900      284512.       ;     C-     H
       1     4   1     0.10900      284512.       ;     C-     H
       1     5   1     0.10900      284512.       ;     C-     H
       :
      41    42                                    ;     O-     H
      41    43                                    ;     O-     H
      44    45                                    ;     O-     H
      44    46                                    ;     O-     H

 [ pairs ]

[ angles ]
; ai  aj  ak  funct      th0         cth
     3     1     2   1     107.800    276.1440     ;     H-     C-     H
     4     1     2   1     107.800    276.1440     ;     H-     C-     H
     5     1     2   1     107.800    276.1440     ;     H-     C-     H
     :
    43    41    42                                 ;     H-     O-     H
    46    44    45                                 ;     H-     O-     H

} 

I tried other input files with changing O.3 to (O.spc and H.spc) and (O.t3p and H.t3p) ,
but force field types of oxygen in H2O were not read. 

Why this problem was occurred? 
Should I fix this topology file? 

Could you tell me this problem solution, please?