On Tuesday, June 25, 2013 8:10 PM, Parker de Waal <parker.dewaa...@kzoo.edu> wrote:
> Now I've been able to successfully convert the two .mol2 files into gromacs > .itp however I am unsure how to convert the .frcmod file as well. I'm sorry, but while topolbuild does convert *.mol2 files into gromacs *.itp files with AMBER parameters, it does not make use of AMBER files. Therefore, topolbuild 1.3 will not convert the *.frcmod files. You should edit your *.itp file with any text editor to change entries according to what is found in the desired *.frcmod file. I should also note that the output from topolbuild 1.3 requires some text editing to be made compatible with GROMACS versions greater than 4.0.* because the arrangement of parameter files within the GROMACS */share/gromacs/top directory was changed and topolbuild has not been updated for that change. Finally, I need to note that for AMBER forcefields in GROMACS naming of atom types was updated to be the standard AMBER atom type names with release of the GROMACS 4.5.* series, but topolbuild 1.3 does not reflect that change either. -- Bruce D. Ray, Ph.D. Associate Scientist IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 -- gmx-users mailing list gmx-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
