[gmx-users] Fatal error: Atomtype F not found
Justin Lemkul
jalemkul at vt.edu
Thu Oct 4 05:16:17 CEST 2012
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
--
========================================
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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