[gmx-users] Re: topolbuild1_3:Illegal characters for size information line in mol2 file.

Bruce D. Ray brucedray at yahoo.com
Thu Jan 26 13:54:15 CET 2012

On Thursday, January 26, 2012 at 12:50 AM, Tom <dnaafm at gmail.com> wrote:

> Dear Bruce and Gromacs Users,

> i am a new user of topolbuild.
> I am trying to use topolbuild to build *top file, but there is a fatal error report:
> -----------------------------------
> ./topolbuild -n lipid -dir /home/machine/TOM/Study/topbuild/topolbuild1_3/topolbuild1_3/dat/gromacs -ff oplsaa

> Fatal error.
> Source code file: readmol2.c, line: 347
> Illegal characters for size information line in mol2 file.
> ------------------------------------
The error is on the line that reads
     295 296

The error means that the line giving the number of atoms and number of bonds
contains characters that are not any of the digits 0123456789, spaces, tabs,
or the line feed that marks end of line.  This typically happens when one
has produced a Microsoft Windows compatible file that terminates lines
with a carriage return and line feed or a Macintosh compatible file that
terminates lines with carriage return instead of line feed.  Probably the file
was generated as Microsoft Windows compatible and you should run the
dos2unix script on the file before submitting it to topolbuild.

If this does not correct the problem, you will need to view the file in a unix
text editor to see where the illegal characters are.

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