I drew a structrue with a pyridine coordinated to Pt (coordinating atom: N). When I put the structure into Chem3D it always showed a lone pair on N which should not exist. I changed the bond between N and Pt to a dative bond and then did MM2 calculation to get the configuration, but when the calculation started it changed the dative bond to a single bond automatically and the lone pair appeared again. What can I do to delete the lone pair on N?

While transferring the 2D information (i.e 2D ChemDraw structure information) to 3D, the 3D model of the structure generated based on defined atoms in Chem3D application (Atom types in the Parameter Tables). When it does not find one, it guesses and uses the closest one. So you have to check the missing element in the Chem3D application. The following links provide you some information regarding this.

http://www.cambridgesoft.com/support/DesktopSupport/KnowledgeBase/FAQ/details/Default.aspx?TechNote=581

http://www.cambridgesoft.com/support/DesktopSupport/KnowledgeBase/FAQ/details/Default.aspx?TechNote=397

If you need further assitance please visit http://www.cambridgesoft.com/contact/support/ to submit a ticket, to get assistance from our Tech Support Team

- PKI Support

How to change atom type? I created a new entry in the MM2 atom type table, but I don't know how to apply the new type.

You will find the basic information in the manual as well as help.

If you need further assitance please visit http://www.cambridgesoft.com/contact/support/ to submit a ticket, to get assistance from our Tech Support Team

- PKI Support