Re: [gmx-users] Fatal error: Atomtype F not found
On 2012-10-04 04:39, 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. Do not combine force fields. Use antechamber and the gromacs conversion script to make a gromacs topology from it (amb2gmx.pl, search on google), then use amber force field in combination with this if you want to dissolve biomolecules or something like that. More organic molecules topologies can be found at http://virtualchemistry.org -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Fatal error: Atomtype F not found
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 : HETATM1 opls_164 HFI A 101 -1.433 -1.291 -0.584 1.00 -0.219790 HETATM2 opls_161 HFI A 101 -1.274 -0.111 -0.039 1.00 0.600750 HETATM3 opls_164 HFI A 101 -1.331 -0.244 1.257 1.00 -0.208510 HETATM4 opls_164 HFI A 101 -2.292 0.639 -0.413 1.00 -0.235630 HETATM5 opls_158 HFI A 101 0.013 0.562 -0.520 1.00 0.064010 HETATM6 opls_078 HFI A 101 0.068 1.864 -0.080 1.00 -0.549590 HETATM7 opls_079 HFI A 101 -0.560 2.404 -0.527 1.00 0.438940 HETATM8 opls_140 HFI A 101 0.014 0.485 -1.602 1.00 0.103910 HETATM9 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 CONECT12 CONECT21345 CONECT32 CONECT42 CONECT52678 CONECT65 CONECT75 CONECT859 10 11 CONECT98 CONECT 108 CONECT 118 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 11 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_1641 0.354 0.142 0.000 1HFI opls_1612 0.369 0.260 0.055 1HFI opls_1643 0.364 0.247 0.184 1HFI opls_1644 0.267 0.335 0.017 1HFI opls_1585 0.498 0.328 0.006 1HFI opls_0786 0.503 0.458 0.050 1HFI opls_0797 0.440 0.512 0.006 1HFI opls_1408 0.498 0.320 -0.102 1HFI opls_1619 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 0.625250.132330.02309 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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
