User 8717ac71bd
29-09-2009 15:44:50
Hi -
I have a piece of software that takes as input Mol2 files with formal charges. Up until the 5.2.x series of Marvin, this was the standard output format for Mol2 files. Now all Mol2 files are output with Partial Charges and I can't find an option to allow me to change this, either in Marvin or molconvert. (I have the Charges Plugin, without the plugin it seems to revert to Formal Charges.)
Is there a way with the Charges Plugin active to get Mol2 files output with Formal Charges?
Thanks.
David
ChemAxon efa1591b5a
01-10-2009 08:22:04
Hi David,
Apparently, mol2 charges are limited to partial charges, explicit formal charges are not supported by mol2/Sybyl. Previous versions of our mol2 export stored formal charges, but that did not comply with Tripos' specification.
Your observation regarding how mol2 export works now and worked in the past is correct. If charge plugin is not available, not licensed, then formal charges are saved in the mol2 file. I am afraid, that this will remain the only, but somewhat clumsy workaround for now, as we do not plan to change this behaviour in the next release of Marvin/Jchem.
In the longer term we may consider to introduce options for formal/partial charge export, though this would raise some compatibility issues, so we have to be careful. Beside of that, we can easier introduce these options in the command line tools as well as in the API, but is somewhat harder in the GUI of MarvinSketch (Save as... dialogue, for instance).
Which ChemAxon tool do you use to export mol2 files? is it the MolConverter? Btw, are you aware of 3rd party programs that allow the user to save formal charges optionally?
What do you think about the SYBYL atom types, could those perhaps solve your problem, at least partly? I mean that there are atom types for carbon cations and positively charged nitrogen atoms... The tools you are using with mol2 files cannot assign formal charges based on a simple valance model?
Apologies for any inconvenience that the new behaviour of mol2 export did cause.
Kind regards,
Miklos