User 2e29183b3d
14-03-2008 17:13:22
Hi,
It is only recently that I discovered that mol2 files generated by molconvert are actually not really proper mol2 files. That is because only some of the atom types are converted to the actual Sybyl atom types. It also DOES NOT state anywhere in the documentation that the currently implemented mol2 conversion does not yield correct mol2 files.
There was an earlier post discussing this issue in early 2007 in this forum, that I am aware of. It was pointed out by somebody from ChemAxon that they didn't have access to Sybyl to check.
The list with all Sybyl atom types and how there are defined is freely available on:
http://www.tripos.com/mol2/atom_types.html
By knowing the connection table it should be no problem to have molconvert output the correct Sybyl atom types, and thereby producing the actual mol2 file format.
Kind regards
It is only recently that I discovered that mol2 files generated by molconvert are actually not really proper mol2 files. That is because only some of the atom types are converted to the actual Sybyl atom types. It also DOES NOT state anywhere in the documentation that the currently implemented mol2 conversion does not yield correct mol2 files.
There was an earlier post discussing this issue in early 2007 in this forum, that I am aware of. It was pointed out by somebody from ChemAxon that they didn't have access to Sybyl to check.
The list with all Sybyl atom types and how there are defined is freely available on:
http://www.tripos.com/mol2/atom_types.html
By knowing the connection table it should be no problem to have molconvert output the correct Sybyl atom types, and thereby producing the actual mol2 file format.
Kind regards