[gmx-users] topolbuild error

[Ray, Bruce D]

On Feb 19, 2015, at 12:44 PM, Zahra Ghanbari <zahraghanbari10 at gmail.com> wrote:

>
>Dear Ray
>I tried to use another .mol2 file. I use USCF chimera to save it.
>
>@<TRIPOS>MOLECULE
>OXL.pdb
>6 5 1 0 0
>SMALL
>NO_CHARGES
>
>
>@<TRIPOS>ATOM
>     1 C1         47.7640   52.0960   49.3000 C.2       1 OXL    0.0000
>     2 C2         48.9620   53.0060   49.8530 C.2       1 OXL    0.0000
>     3 O1         47.5730   51.0150   49.8280 O.co2     1 OXL    0.0000
>     4 O2         49.5800   52.4680   50.7770 O.co2     1 OXL    0.0000
>     5 O3         47.0570   52.5150   48.3410 O.co2     1 OXL    0.0000
>     6 O4         49.0630   54.1080   49.2490 O.co2     1 OXL    0.0000
>@<TRIPOS>BOND
>    1    1    2 2
>    2    1    3 2
>    3    1    5 2
>    4    2    4 2
>    5    2    6 2
>@<TRIPOS>SUBSTRUCTURE
>    1 OXL     1 RESIDUE           4 A     OXL     0 ROOT
>
>Unfortunately, I confronted the new error:
>
>Fatal error.
>Source code file: readmol2.c, line: 419
>File read to end without finding molecule record reading mol2 file.
>I am looking forward to getting your guidance.

Interesting.  The only time I've seen that error arise is when there
were extraneous characters in the file, typically because the file
was made under Windows.  Running dos2unix on such files typically
removed the problem.

I've been busy and have not actually worked on topolbuild 1.3 since
early 2011.


-- 
Bruce D. Ray, Ph.D.
Associate Scientist
IUPUI
Physics Dept.
402 N. Blackford St., Rm. LD-061
Indianapolis, IN  46202