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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