[gmx-users] Problem with topolbuild

[Bruce D. Ray]

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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