[gmx-users] grompp error : Atomtype HC not found

[Atila Petrosian]

Hi gromacs users,

I am doing MD simulation of my system (DPPC lipid + 2 drug molecules +
water molecules) using gromacs 2019.

I used ATB for drug molecules and Tieleman's web site for lipid molecules.
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My topology file is as follows:
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#include "ffgmx.itp"
#include "lipid.itp"
#include "dppc.itp"
#include "lig.itp"

#ifdef POSRES_LIG
#include "lig_posre.itp"
#endif

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000
#endif

[ system ]
; name
dppc/lig/lig/sol

[ molecules ]
; Compound        #mols
DPP        128
LIG          2
SOL       7173
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My lig.itp file is as follows:
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.
.
.
.
;
[ moleculetype ]
; Name   nrexcl
LIG     3

[ atoms ]
;  nr  type  resnr  resid  atom  cgnr  charge    mass
    1    HC    1    LIG    H27    1    0.131   1.0080
    2  CAro    1    LIG    C24    2   -0.130  12.0110
    3  CAro    1    LIG    C23    3   -0.130  12.0110
    4    HC    1    LIG    H26    4    0.131   1.0080
    5  CAro    1    LIG    C22    5   -0.119  12.0110
    6    HC    1    LIG    H25    6    0.135   1.0080
    7  CAro    1    LIG    C21    7   -0.039  12.0110
    8  CAro    1    LIG    C26    8   -0.119  12.0110
    9    HC    1    LIG    H29    9    0.135   1.0080
   10  CAro    1    LIG    C25   10   -0.130  12.0110
   11    HC    1    LIG    H28   11    0.131   1.0080
   12     C    1    LIG    C18   12   -0.051  12.0110
   13   CH2    1    LIG    C19   13    0.055  14.0270
   14   CH3    1    LIG    C20   14    0.020  15.0350
   15  CAro    1    LIG    C11   15   -0.025  12.0110
   16  CAro    1    LIG    C12   16   -0.040  12.0110
   17  CAro    1    LIG    C13   17   -0.117  12.0110
   18    HC    1    LIG    H15   18    0.137   1.0080
   19  CAro    1    LIG    C14   19   -0.133  12.0110
   20    HC    1    LIG    H16   20    0.131   1.0080
   21  CAro    1    LIG    C15   21   -0.129  12.0110
   22    HC    1    LIG    H17   22    0.131   1.0080
   23  CAro    1    LIG    C16   23   -0.133  12.0110
   24    HC    1    LIG    H18   24    0.131   1.0080
   25  CAro    1    LIG    C17   25   -0.117  12.0110
   26    HC    1    LIG    H19   26    0.137   1.0080
   27  CAro    1    LIG     C8   27   -0.076  12.0110
   28  CAro    1    LIG     C7   28   -0.079  12.0110
   29    HC    1    LIG    H12   29    0.139   1.0080
   30  CAro    1    LIG     C6   30   -0.184  12.0110
   31    HC    1    LIG    H11   31    0.143   1.0080
   32  CAro    1    LIG     C5   32    0.087  12.0110
   33  CAro    1    LIG    C10   33   -0.184  12.0110
   34    HC    1    LIG    H14   34    0.143   1.0080
   35  CAro    1    LIG     C9   35   -0.079  12.0110
   36    HC    1    LIG    H13   36    0.139   1.0080
   37    OE    1    LIG     O1   37   -0.219  15.9994
   38   CH2    1    LIG     C4   38    0.149  14.0270
   39   CH2    1    LIG     C3   39    0.101  14.0270
   40  NTer    1    LIG     N1   40   -0.267  14.0067
   41   CH3    1    LIG     C1   41    0.097  15.0350
   42   CH3    1    LIG     C2   42    0.097  15.0350
; total charge of the molecule:   0.000
[ bonds ]
;  ai   aj  funct   c0         c1
    1    2    2   0.1090   1.2300e+07
    2    3    2   0.1390   8.6600e+06
.
.
.
.
.
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After using command: gmx solvate -cp final.gro -cs spc216.gro -p topol.top
-o system.gro, I encountered with the following error:
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ERROR 1 [file lig.itp, line 65]:
  Atomtype HC not found
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How to resole it?

Best,
Atila