[gmx-users] Fatal error: Atomtype F not found

[Justin Lemkul]

On 10/3/12 10:43 PM, Nur Syafiqah Abdul Ghani wrote:
> Dear Users,
>
> Right now i already done for creating the a gro file from antechamber
> to gromacs format of my molecule which is hexafluoroisopropanol.
> But when i want to minimize it in vacuum it show atomtype F not found.
> Im using oplsaa force field and i already change the atom type
> according to the force field.
>
> Below are my files that i need to used for my minimization :
>
> PDB file :
>
> HETATM    1  opls_164  HFI A  101     -1.433  -1.291  -0.584  1.00  -0.219790
> HETATM    2  opls_161  HFI A  101     -1.274  -0.111  -0.039  1.00   0.600750
> HETATM    3  opls_164  HFI A  101     -1.331  -0.244   1.257  1.00  -0.208510
> HETATM    4  opls_164  HFI A  101     -2.292   0.639  -0.413  1.00  -0.235630
> HETATM    5  opls_158  HFI A  101      0.013   0.562  -0.520  1.00   0.064010
> HETATM    6  opls_078  HFI A  101      0.068   1.864  -0.080  1.00  -0.549590
> HETATM    7  opls_079  HFI A  101     -0.560   2.404  -0.527  1.00   0.438940
> HETATM    8  opls_140  HFI A  101      0.014   0.485  -1.602  1.00   0.103910
> HETATM    9  opls_161  HFI A  101      1.289  -0.122  -0.036  1.00   0.652070
> HETATM   10  opls_164  HFI A  101      2.323   0.430  -0.620  1.00  -0.216720
> HETATM   11  opls_164  HFI A  101      1.282  -1.395  -0.353  1.00  -0.223970
> HETATM   12  opls_164  HFI A  101      1.450  -0.022   1.254  1.00  -0.205480
> CONECT    1    2
> CONECT    2    1    3    4    5
> CONECT    3    2
> CONECT    4    2
> CONECT    5    2    6    7    8
> CONECT    6    5
> CONECT    7    5
> CONECT    8    5    9   10   11
> CONECT    9    8
> CONECT   10    8
> CONECT   11    8   12
> CONECT   12   11
> END
>
> also the topology ;
>
> ; Include forcefield parameters
> #include "oplsaa.ff/forcefield.itp"
> ; Include organic solvent
> #include "hfi.itp"
> ; Include water topology
> #include "oplsaa.ff/spc.itp"
> #ifdef POSRER_WATER
> ; Position restraint for each water oxygen
> [position_restraints]
> ; i funct  fcx   fcy   fcz
>    1    1   1000  1000  1000
> #endif
> [system]
> ;Name
> solute
> [molecules]
> ;Compound  #mols
> HFI         1
>
>
> gro file;
>
> solvent_HFI.gro.gro created by rdparm2gmx.pl Sat May 28 10:25:18 MYT 2005
>   12
>      1HFI   opls_164    1   0.354   0.142   0.000
>      1HFI   opls_161    2   0.369   0.260   0.055
>      1HFI   opls_164    3   0.364   0.247   0.184
>      1HFI   opls_164    4   0.267   0.335   0.017
>      1HFI   opls_158    5   0.498   0.328   0.006
>      1HFI   opls_078    6   0.503   0.458   0.050
>      1HFI   opls_079    7   0.440   0.512   0.006
>      1HFI   opls_140    8   0.498   0.320  -0.102
>      1HFI   opls_161    9   0.626   0.260   0.055
>      1HFI   opls_164   10   0.729   0.315  -0.004
>      1HFI   opls_164   11   0.625   0.132   0.023
>      1HFI   opls_164   12   0.642   0.270   0.184
>      0.62525    0.13233    0.02309
>
> is there something wrong of my file?

Your .pdb and .gro files call opls_* atom names, which are actually atom types. 
  Do not confuse the two.

> Why it cant recognize the F atom??

Without seeing the contents of hfi.itp, it's hard to say aside from the general 
statement that you're using an atom type that does not exist.  I suspect you've 
confused atom types and names, given the coordinate files shown.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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