[gmx-users] gro to itp file

[Anubha Agrawal]

Hello gmx users,

Please ignore my previous post. My query is following-

I've prepared a coordinate file in .gro format using pdb2gmx. I obtained
the pdb from openbabel online server and used it for pdb2gmx command.
Further, I've identified CHARMM36 atom types for my molecule. This molecule
is one of the model compounds for lignin. I've included the new residue
information of the molecule in .rtp file. Now I want to generate a GROMACS
topology file for the same. Any help will be appreciated.

The .gro file is:

43

1LIG O 1 0.300 0.000 0.000

1LIG O 2 0.387 -0.050 0.000

1LIG O 3 0.500 0.173 0.000

1LIG O 4 0.783 0.037 0.000

1LIG O 5 0.200 -0.173 0.000

1LIG O 6 0.783 -0.163 0.000

1LIG C 7 0.350 0.087 0.000

1LIG C 8 0.437 0.037 0.000

1LIG C 9 0.523 -0.013 0.000

1LIG C 10 0.400 0.173 0.000

1LIG C 11 0.610 0.037 0.000

1LIG C 12 0.523 -0.113 0.000

1LIG C 13 0.200 0.000 0.000

1LIG C 14 0.696 -0.013 0.000

1LIG C 15 0.610 -0.163 0.000

1LIG C 16 0.696 -0.113 0.000

1LIG C 17 0.150 -0.087 0.000

1LIG C 18 0.150 0.087 0.000

1LIG C 19 0.050 -0.087 0.000

1LIG C 20 0.050 0.087 0.000

1LIG C 21 0.000 0.000 0.000

1LIG C 22 0.870 -0.013 0.000

1LIG C 23 0.300 -0.173 0.000

1LIG H 24 0.263 0.137 0.000

1LIG H 25 0.487 0.123 0.000

1LIG H 26 0.400 0.273 0.000

1LIG H 27 0.313 0.223 0.000

1LIG H 28 0.610 0.137 0.000

1LIG H 29 0.437 -0.163 0.000

1LIG H 30 0.287 -0.050 0.000

1LIG H 31 0.610 -0.263 0.000

1LIG H 32 0.200 0.173 0.000

1LIG H 33 0.550 0.260 0.000

1LIG H 34 0.000 -0.173 0.000

1LIG H 35 -0.000 0.173 0.000

1LIG H 36 -0.100 -0.000 0.000

1LIG H 37 0.783 -0.263 0.000

1LIG H 38 0.970 -0.013 0.000

1LIG H 39 0.920 0.073 0.000

1LIG H 40 0.870 -0.113 0.000

1LIG H 41 0.387 -0.223 0.000

1LIG H 42 0.300 -0.273 0.000

1LIG H 43 0.350 -0.087 0.000

0.00000 0.00000 0.00000


Residue information used in .rtp file is-

[ LIG ]
   [ atoms ]
HP      HP1      0.115
CA      CA1      -0.115
CA      CA2      -0.115
HP      HP2      0.115
CA      CA3      -0.115
HP      HP3      0.115
CA      CA4      0.22
OC30A   OC30A1   -0.39
CT3     CT32     -0.1
HA      HA07     0.09
HA      HA08     0.09
HA      HA09     0.09
CA       CA5     0.22
CA       CA6     -0.115
HP       HP6     0.115
OC30A   OC30A2   -0.39
CT1     CT11     0.22
CT2     CT21     0.05
HA      HA00     0.09
HA      HA01     0.09
OH1      OH11    -0.65
H        H1      0.42
HA       HA02    0.09
CT1      CT12    0.14
OH1      OH12    -0.65
HA       HA03    0.09
H        H2      0.42
CA       CA7     0.000
CA       CA8     -0.115
CA       CA9     -0.115
HP      HP8      0.115
HP       HP9     0.115
CA       CA10    0.11
OH1      OH13    -0.54
H        H3      0.43
CA       CA11    0.22
OC30A   OC3AO3   -0.39
CT3      CT31    -0.1
HA       HA04    0.09
HA       HA05    0.09
HA       HA06    0.09
CA       CA12    -0.115
HP       HP12    0.115

[ BONDS ]
CA1 HP1
CA1 CA2
CA2 HP2
CA2 CA3
CA3 HP3
CA3 CA4
CA4 CA5
CA5 CA6
CA6 CA1
CA6 HP6
CA5 OC30A2
CA4 OC30A1
OC30A1 CT32
CT32 HA07
CT32 HA08
CT32 HA09
OC30A2 CT11
CT11 CT21
CT21 HA00
CT21 HA01
CT21 OH11
OH11 H1
CT11 HA02
CT22 CT12
CT12 OH12
CT12 HA03
CT12 CA7
CA7 CA8
CA8 HP8
CA8 CA9
CA9 HP9
CA9 CA10
CA10 CA11
CA11 CA12
CA12 CA7
CA12 HP12
CA11 OC30A3
OC30A3 CT31
CT31 HA04
CT31 HA05
CT31 HA06
CA10 OH13
OH13 H3
OH12 H2

Thanks

Regards’

Anubha