[gmx-users] Fatal Error: Atom Type

[Yang Ye]

You may use -pp <file name> for grompp to have a look at the final 
topology file after merging.

Amol D. Atre wrote:

>Hello all,
>
>Trying to solvate 1 molecule of NH3 in 4 molecules of H2O
>
>NH3.itp ---->
>
>#ifndef _FF_GROMOS96
>
>[ atomtypes ]
>;   type      mass    charge    ptype       c6            c12
>      NL    14.0067    -0.69     A	2.6169e-3      2.5231e-6
>       H      1.008    -0.82     A	2.6170e-3      2.6330e-6
>
>#endif
>
>[ moleculetype ]
>; name  nrexcl
>Ammonia        2
>
>[ atoms ]
>;   nr  type    resnr   residu  atom    cgnr    charge	mass
>#ifdef _FF_GROMOS96
>1       NL     1       LYS    NL1      1        0.176 14.0067
>2       H      1       ABU    H2       1       -0.574  1.008
>3       H      1       ABU    H3       1       -0.574  1.008
>4       H      1       ABU    H4       1        0.398  1.008
>#else
>1       NL     1       LYS    NL1      1        0.29  14.0067
>2       H      1       ABU    H2       1       -0.69   1.008
>3       H      1       ABU    H3       1       -0.69   1.008
>4       H      1       ABU    H4       1        0.40   1.008
>#endif
>
>;[ bonds ]
>;  ai  aj funct           c0           c1
>1       2	1	   0.13600     376560.
>2       3	1	   0.10000     313800.
>
>;[ angles ]
>;  ai    aj    ak       funct   c0      c1
>    1     2     3       1       108.53  397.5
>
>H2O.itp ---->
>
>#ifndef _FF_GROMOS96
>
>[ atomtypes ]
>;   type      mass     charge
>       HW     1.008      0.41
>       OW    15.9994    -0.82
>
>#endif
>
>[ moleculetype ]
>; name  nrexcl
>Water        4
>
>[ atoms ]
>;   nr  type    resnr   residu  atom    cgnr    charge	mass
>#ifdef _FF_GROMOS96
>1       OW     1       SOL    OW1       1       -0.82   15.9994
>2       HW     1       SOL    H2        1        0.41    1.008
>3       HW     1       SOL    H3        1        0.41    1.008
>4       OW     2       SOL    OW4       1       -0.82   15.9994
>5       HW     2       SOL    HW5       1        0.41    1.008
>6       HW     2       SOL    HW6       1        0.41    1.008
>7       OW     3       SOL    OW7       1       -0.82   15.9994
>8       HW     3       SOL    HW8       1        0.41    1.008
>9       HW     3       SOL    HW9       1        0.41    1.008
>10      OW     4       SOL    OW10      1       -0.82   15.9994
>11      HW     4       SOL    HW11      1        0.41    1.008
>12      HW     4       SOL    HW12      1        0.41    1.008
>#else
>1       OW     1       SOL    OW1       1       -0.82   15.9994
>2       HW     1       SOL    H2        1        0.41    1.008
>3       HW     1       SOL    H3        1        0.41    1.008
>4       OW     2       SOL    OW4       1       -0.82   15.9994
>5       HW     2       SOL    HW5       1        0.41    1.008
>6       HW     2       SOL    HW6       1        0.41    1.008
>7       OW     3       SOL    OW7       1       -0.82   15.9994
>8       HW     3       SOL    HW8       1        0.41    1.008
>9       HW     3       SOL    HW9       1        0.41    1.008
>10      OW     4       SOL    OW10      1       -0.82   15.9994
>11      HW     4       SOL    HW11      1        0.41    1.008
>12      HW     4       SOL    HW12      1        0.41    1.008
>#endif
>
>NH3.top ---->
>
>#include "ffgmx.itp"
>#include "NH3.itp"
>
>[ system ]
>Ammonia
>
>[ molecules ]
>Ammonia		1
>
>H2O.top ---->
>
>#include "ffgmx.itp"
>#include "H2O.itp"
>
>[ system ]
>Water
>
>[ molecules ]
>Water		4
>
>topol.top ---->
>
>#include "ffgmx.itp"
>#include "NH3.itp"
>#include "H2O.itp"
>
>[ system ]
>Ammonia-Water in water
>[ molecules ]
>Ammonia		1
>Water		4
>SOL               109
>
>Command line: genbox -cp NH3.gro -cs H2O.gro -o NH3-H2O.gro -p topol.top
>-box 2 2 2
>
>to solvate.
>
>Then running grompp -v getting ---->
>
>Fatal error: Atomtype '2' not found!
>
>What must be going wrong, can anybody help?
>
>Thanks in advance.
>
>Regards,
>Amol D. Atre.
>Lab No.A002,
>Chemical Engineering Department,
>Mumbai University Institute of Chemical Technology,
>Matunga(E), Mumbai-400019.
>
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