[gmx-users] Problem with topolbuild

[Gunnar Widtfeldt Reginsson]

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 <brucedray at yahoo.com> wrote:

> On Sun, November 8, 2009 at 5:31:30 PM, Gunnar Widtfeldt Reginsson
> <reginsson at 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
>
>
>
> --
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