[gmx-users] Hydrogens missing during parameterization

[Anirban Ghosh]

Hi ALL,

I have a ligand LDOPA with 25 atoms (including all hydrogens).:
-------------------------------------------------------------------------------------------------------------------------------------------
DAH COORDS
   25
    1DAH  O        1   5.988   5.216   9.128
    1DAH  C        2   5.980   5.110   9.194
    1DAH  OXT      3   5.951   4.985   9.139
    1DAH  CA       4   6.001   5.107   9.349
    1DAH  HA       5   5.935   5.027   9.384
    1DAH  N        6   6.140   5.064   9.387
    1DAH  H2       7   6.161   4.977   9.343
    1DAH  H3       8   6.137   5.056   9.486
    1DAH  H1       9   6.206   5.133   9.356
    1DAH  CB      10   5.952   5.236   9.422
    1DAH  HB1     11   5.985   5.320   9.362
    1DAH  HB2     12   5.999   5.231   9.520
    1DAH  CG      13   5.802   5.258   9.450
    1DAH  CD2     14   5.761   5.333   9.565
    1DAH  HD2     15   5.836   5.375   9.632
    1DAH  CE2     16   5.623   5.353   9.592
    1DAH  OE2     17   5.589   5.425   9.704
    1DAH  HE2     18   5.672   5.454   9.752
    1DAH  CZ      19   5.523   5.297   9.503
    1DAH  OZ      20   5.387   5.314   9.525
    1DAH  HZ      21   5.335   5.268   9.453
    1DAH  CE1     22   5.564   5.223   9.389
    1DAH  HE1     23   5.489   5.181   9.321
    1DAH  CD1     24   5.701   5.203   9.362
    1DAH  HD1     25   5.731   5.146   9.274
   1.02033   1.02033   1.02033
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

 I derived the topology file from PRODRG server. However the .itp file is
giving only 22 atoms definition and 3 of the hydrogen atoms are missing:

---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
DAH      3

[ atoms ]
;   nr      type  resnr resid  atom  cgnr   charge     mass
     1        OM     1  DAH       O     1   -0.715  15.9994
     2         C     1  DAH       C     1    0.387  12.0110
     3        OM     1  DAH     OXT     1   -0.716  15.9994
     4       CH1     1  DAH      CA     1    0.178  13.0190
     5        NL     1  DAH       N     1    0.683  14.0067
     6         H     1  DAH      H2     1    0.010   1.0080
     7         H     1  DAH      H3     1    0.010   1.0080
     8         H     1  DAH      H1     1    0.011   1.0080
     9       CH2     1  DAH      CB     1    0.152  14.0270
    10         C     1  DAH      CG     2   -0.020  12.0110
    11       CR1     1  DAH     CD2     2    0.001  12.0110
    12        HC     1  DAH     HD2     2    0.019   1.0080
    13         C     1  DAH     CE2     3    0.130  12.0110
    14        OA     1  DAH     OE2     3   -0.197  15.9994
    15         H     1  DAH     HE2     3    0.051   1.0080
    16         C     1  DAH      CZ     3    0.130  12.0110
    17        OA     1  DAH      OZ     3   -0.197  15.9994
    18         H     1  DAH      HZ     3    0.051   1.0080
    19       CR1     1  DAH     CE1     3    0.001  12.0110
    20        HC     1  DAH     HE1     3    0.031   1.0080
    21       CR1     1  DAH     CD1     4    0.000  12.0110
    22        HC     1  DAH     HD1     4    0.000   1.0080

[ bonds ]
----------------------------------------------------------------------------------------------------------------------------------------------------------------
So you can see that HA, HB2 and HB3 hydrogens are missing here. So I am
getting error messages popped by grompp commands. How can I get the
definition of those missing 3 H atoms? Is it ok if I delete those 3 H atoms
from my .gro file and proceed? If not then how to derive parameters for
them? Any suggestion is welcome.
Thanks a lot in advance.

Regards,

Anirban
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