invalid energy specification in molfile header

Hi,
I have a legacy  SDF files,in which have 400 compounds,but it always have errors opening them with Mview or MSketch or cxcalc,

error:Read error after molecule 0:
invalid energy specification in molfile header:"guire and ro"

the original data of the SDF file opened with TXT, we get a molecule:

91-08-7
Prepared by Jeroen Kazius, Ross McGuire and Roberta Bursi.

 19 19                          1 V2000
    1.2094   -0.1551   -0.0022 C   0  0  0
   -0.0001   -0.8598   -0.0013 C   0  0  0
    1.1979    1.3183   -0.0020 C   0  0  0
    2.3609   -0.8109    0.0024 N   0  0  0
   -1.2094   -0.1551   -0.0003 C   0  0  0
   -0.0001   -2.3668   -0.0020 C   0  0  0
   -0.0002    2.0035   -0.0010 C   0  0  0
    3.4398   -0.1795    0.0016 C   0  0  0
   -1.1978    1.3185   -0.0002 C   0  0  0
   -2.3609   -0.8109    0.0001 N   0  0  0
    4.4823    0.4306    0.0009 O   0  0  0
   -3.4397   -0.1795    0.0009 C   0  0  0
   -4.4823    0.4307    0.0018 O   0  0  0
    2.0909    1.8410    0.0000 H   0  0  0
   -1.0348   -2.3668    0.0000 H   0  0  0
   -0.0001   -3.4015    0.0000 H   0  0  0
    1.0346   -2.3668    0.0000 H   0  0  0
   -0.0002    3.0382    0.0000 H   0  0  0
   -2.0908    1.8412    0.0000 H   0  0  0
  1  2  1  0
  1  3  2  0
  1  4  1  0
  2  5  2  0
  2  6  1  0
  3  7  1  0
  4  8  2  0
  5  9  1  0
  5 10  1  0
  8 11  2  0
 10 12  2  0
 12 13  2  0
  7  9  2  0
  3 14  1  0
  6 15  1  0
  6 16  1  0
  6 17  1  0
  7 18  1  0
  9 19  1  0
M  END
>  <Ames test categorisation>
mutagen

$$$$

if i swap the header

"

91-08-7
Prepared by Jeroen Kazius, Ross McGuire and Roberta Bursi.

"

with 

"
  Marvin  09301010362D         
"

and the molecule of the file can be opened.

but i want  to open the file all, so what i can do?

Hi,

 

I copied the the text that you said was from your original file, and I could paste it to MarvinSketch without any problem. Please send your file (the firs 2-3 records are enough, but if you compress it, it will be very small, so you can even send the whole SDFile) in its original format as an attachment to be able to reproduce the bug.

 

Thank you and best regards,

 

Akos

 

Hi,

 

I found the source of this issue in the documentation of the CTFile formats:

 

http://www.symyx.com/downloads/public/ctfile/ctfile.pdf

 

The second line of the header block of your records is wrong, according to page 70:

Line 2:
This line has the format:
IIPPPPPPPPMMDDYYHHmmddSSssssssssssEEEEEEEEEEEERRRRRR
(FORTRAN: A2<--A8--><---A10-->A2I2<--F10.5-><---F12.5--><-I6-> )
User's first and last initials (l), program name (P), date/time (M/D/Y,H:m), dimensional codes (d) such as 2D or 3D, scaling factors (S, s), energy (E) if modeling program input, internal registry number (R)
The “dimensional code” is maintained explicitly. Thus “3D” really means 3D, although “2D” will be interpreted as 3D if any non-zero Z-coordinates are found.
Note: A blank line can be substituted for line 2.

 

As you can see, between the 35th and 46th characters the energy is expected, but in your file there is the "Guire and Ro" text instead.

 

Best regards,

 

Akos

Thanks a lot Akos ! 

I have solved the problem as your clew!

Thanks very much again !