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

[Justin Lemkul]

On 2/13/20 8:56 AM, Atila Petrosian wrote:
> 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.

ATB uses a custom version of GROMOS96 that uses new atom types. You need 
to use their force field files.

> ---------------------------------------
> My topology file is as follows:
> ---------------------------------------
> #include "ffgmx.itp"

There is no reason to use this totally obsolete force field.

-Justin

> #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
> ---------------------------------------
> My lig.itp file is as follows:
> ---------------------------------------
> .
> .
> .
> .
> ;
> [ 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
> .
> .
> .
> .
> .
> ---------------------------------------
> After using command: gmx solvate -cp final.gro -cs spc216.gro -p topol.top
> -o system.gro, I encountered with the following error:
> ---------------------------------------
> ERROR 1 [file lig.itp, line 65]:
>    Atomtype HC not found
>    ---------------------------------------
>
> How to resole it?
>
> Best,
> Atila

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
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