Dear All,
Having a great deal of trouble trying to find a workaround to this issue. It's been posted about before and it's been deemed unecessary to fix, however I feel this bug is something that needs attending to.
Strictly speaking, mol2 files should be self-sufficient units which can be plugged into other tools for visualisation/modification/simulation. The format of the mol2 file output from leap is incorrect, both in terms of how it deals with connectivity (double/triple bonds labelled incorrectly as single bonds) and how it labels atoms (enters data other than the standard SYBYL atom types). This means that mol2 files are only useable for amber, which is giving me a lot of trouble (I am using the c++ OpenBabel distributable for atomic modifications).
If anyone else has encountered this issue and knows of a workaround then please let me know! I need to be able to obtain self-sufficient mol2 (or any other format with well-defined connectivity/bond-order) in order for OpenBabel to be able to interpret structures correctly.
Cheers,
Nick
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Received on Tue Mar 18 2014 - 08:30:03 PDT
