[gmx-users] topolbuild

Bruce D. Ray brucedray at yahoo.com
Mon May 5 14:11:16 CEST 2014

On Sunday, May 4, 2014, at 3:04 AM Hossein Lanjanian <hossein.lanjanian at gmail.com> wrote:

> hi
> We installed topolbuild
> topolbuild version 1.3
> Command line:
>      /home/Hossein/Desktop/topolbuild1_3/src/topolbuild -n test -dir
> ./topolbuild1_3/dat/gromacs -ff oplsaa
> Fatal error.
> Source code file: readmol2.c, line: 639
> Incomplete mol2 file after bonds record.:
> we would like to know, what is the origin of this error.
> -- 
> With The Best
> H.Lanjanian
> -----------------------------------------------------------------------
> Hossein Lanjanian,
> Ph.D. student
> Laboratory of Systems Biology and Bioinformatics
> (LBB)
> Institute of Biochemistry and Biophysics (IBB), University of
> Tehran
> Tehran, Iran
> http://LBB.ut.ac.ir     http://ibb.ut.ac.ir
> H.Lanjanian at ut.ac.ir

Your mol2 file does not have any mol2 lines after the bonds
records.  At the end of the bonds list, a proper mol2 file
has a line that begins with, "@<TRIPOS>" and ends with the
unix end of line.  For most mol2 files, this is line reads,
"@<TRIPOS>SUBSTRUCTURE", but unless the mol2 file header
record calls for some form of restraints, the program only
checks for the initial tag.  To correct your file, you
only need to add the appropriate line, terminated by an
end of line, to your file.

I hope that helps. 

Bruce D. Ray, Ph.D.
Associate Scientist
Physics Dept.
402 N. Blackford St.
Indianapolis, IN 46202-3273

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