Hello,
I am having problems in converting PDB files to mdl on Linux. I tried a couple of versions of babel. The main problem is that the type of bond info is different. For example, if I use 1A07.pdb I get all single bonds whereas the windows version as was given to me by someone else gives double as well as tripple bonds. I had the same problem with mol and mol2 formats too.

I am using Mandriva 2006.0 and Mandrake 10.2 and both give the same problems.

Output reg bonds from windows version that was given to me:
1 2 1 0 0 0
1 7 1 0 0 0
1 8 1 0 0 0
1 9 1 0 0 0
2 3 1 0 0 0
2 5 1 0 0 0
3 4 2 0 0 0
3 11 1 0 0 0
5 6 1 0 0 0
6 10 1 0 0 0
11 12 1 0 0 0
11 19 1 0 0 0
12 13 1 0 0 0
12 15 1 0 0 0


Output from Linux version:
M V30 1 1 9 1
M V30 2 1 8 1
M V30 3 1 1 7
M V30 4 1 1 2
M V30 5 1 2 3
M V30 6 1 2 5
M V30 7 1 3 11
M V30 8 1 3 4
M V30 9 1 5 6
M V30 10 1 10 6
M V30 11 1 19 11
M V30 12 1 11 12
M V30 13 1 15 12
M V30 14 1 12 13


I am trying to obtain information on all bonds that are present. But I am only getting single bonds from mol, mol2 and mdl formats. I would like to know if this is a bug or if I am going the wrong way.

Thanks in advance for any help.
-S

PS: Usage:

For mol format (similar for mdl and mol2):
$ babel -x3 -ipdb 1A07.pdb -omol 1A07.mol