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Exporting molecule file with charges ... Log Out | Topics | Search
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Author Message
Ihosvany Camps
Unregistered guest
Posted on Friday, October 23, 2009 - 3:05 pm:   


I would like to know if it is possible to export a MOL or PDB file with the calculated charges included.

Best regards,

JR Schmidt
Username: Schmidt

Post Number: 121
Registered: 11-2006
Posted on Sunday, October 25, 2009 - 6:28 pm:   

This is not currently possible. I would have to look at the MOL and PDB file format specifications to even check whether this is possible. (I believe it is for PDB, not sure about MOL). This may be implemented in a future version.
John Keller
Unregistered guest
Posted on Thursday, June 26, 2014 - 3:53 am:   

The MDL MOL file format specification contains atom charge information in two places: in the second column to the right of the atom symbol, and in a "M CHG nnn" line preceding "M end". WebMO does *export* a charge value in the atom line, however it ignores charge values in this location when *importing*. WebMO sometimes makes terrible guesses about charge, and it would be nice to start with reasonable values. For example, try the FBCl+ ion, in which the B is given a 3+ charge in the exported MOL file.
JR Schmidt
Username: Schmidt

Post Number: 407
Registered: 11-2006
Posted on Saturday, July 19, 2014 - 2:56 pm:   


To be clear: to you think that WebMO should be IMPORTING the charge from the MOL file, or NOT EXPORTING a charge?

"Guessing" the charge is hard for exotic species like those you mention. For the most part we area doing it using standard formal charge rules.

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