Thank you. I am new to Unix commands, so could you please explain a little more how I am to apply these bug fixes?
Thanks On Mon, Nov 9, 2009 at 12:51 PM, Bruce D. Ray <bruced...@yahoo.com> wrote: > On Sun, November 8, 2009 at 5:31:30 PM, Gunnar Widtfeldt Reginsson > <regins...@gmail.com> wrote: > > > > I have a small organic molecule that I processed with antechamber using > the gaff forcefield > > and got a mol2 file. I want to get .gro and. itp files from this to use > with GROMACS. So I tried > > to use the program "topolbuild version 1.2" from the GROMACS website. > > > > when I execute the command: > > "topolbuild -dir ../ -ff gaff -n nameofmolecule -r SL -last 1241 -resnum > 40" > > I get this error message: > > Fatal error. > > Source code file: readmol2.c, line: 109 > > Atomic symbol cc in atom type not found. > > > > When I excecute the topolbuild above I use -dir ../ because that should > take the program > > to the directory containing dat/antechamber and etc. which actually comes > with the > > topolbuild 1.2 package > > > > I don't know what to do and I have tried searching this mailing list and > google without sucess. > > > > Can someone please help me? > > First, the mol2 file that you are using is not syntactically correct > because it is using > gaff atom types and not Tripos' Sybyl atom types. A syntactically correct > mol2 file > would not have atom type cc. Please process your organic molecule against > the > Sybyl force field to get a correct mol2 file. > > Second, there are a number of bug fixes I have placed in this list for > version 1.2.1 > which is the version I hope you are using. The following diffs should be > applied: > > diff topolbuild1_2_1/src/Makefile topolbuild1_2_2/src/Makefile > 22,23c22,29 > < $(PROGRAM): $(SOURCES) > < $(CC) -o $(PROGRAM) $(CFLAGS) $(SOURCES) -lm > --- > > $(PROGRAM): $(OBJECTS) > > $(CC) -o $(PROGRAM) $(CFLAGS) $(OBJECTS) -lm > > > > clean: > > rm -f *.o > > > > dist_clean: > > rm -f *.o $(PROGRAM) > diff topolbuild1_2_1/src/Makefile.G4OsX topolbuild1_2_2/src/Makefile.G4OsX > 22,23c22,29 > < $(PROGRAM): $(SOURCES) > < $(CC) -o $(PROGRAM) $(CFLAGS) $(SOURCES) -lm > --- > > $(PROGRAM): $(OBJECTS) > > $(CC) -o $(PROGRAM) $(CFLAGS) $(OBJECTS) -lm > > > > clean: > > rm -f *.o > > > > dist_clean: > > rm -f *.o $(PROGRAM) > diff topolbuild1_2_1/src/ring_detect.c topolbuild1_2_2/src/ring_detect.c > 450c450 > < ar_set[(t_ring_atomno[i][j])][3]++; > --- > > ar_set[(t_ring_atomno[i][k])][3]++; > diff topolbuild1_2_1/src/topolbuild.c topolbuild1_2_2/src/topolbuild.c > 440c440 > < max_rng = num_bonds/2; > --- > > max_rng = 3 * num_bonds/4; > > Also, when using Gromacs force fields, the defaults definition line needs > to > be changed from: > 1 2 yes 0.5 0.8333 > to: > 1 1 no 1.0 1.0 > > Unfortunately, I did not allow for different defaults for different force > fields > in that version. The next version will correct that as well as adding > OPLSAA > to the suite of force fields available. > > > Sincerely, > > > -- > 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/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/mailing_lists/users.php >
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