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Topic Title: why the structure isn't correct when I did MM2 optimization in chem3d?
Topic Summary: Different structure with Chem3D MM2 optimization
Created On: 10/20/2020 3:09 AM
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 10/20/2020 3:09 AM
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jieun

Posts: 4
Joined: 10/20/2020

hi

I have a question with MM2 optimization function of chem3d.

I draw molecule and do MM2 optimization but the structure doesn't correspond with the structure that I expect. (The structure I expect is equal to the result that calculate with dft.)

why does it happen? what is the problem?

 10/20/2020 4:22 AM
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CS RNA

Posts: 683
Joined: 2/25/2009

We are not sure about the product as well as the version of product you have installed on your machine. Also not sure about the structure you tried.

While transferring the 2D information (i.e 2D ChemDraw structure information) to 3D, the 3D model of the structure is 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

Also you can get the information regarding defining atoms in Chem3D Help as well as from the user manual.

If yo still run in to any problem, please visit http://informatics.perkinelmer.com/Support/Contact/ to submit a ticket (or send an email to informatics.support@perkinelmer.com) along with the sample structure, to get assistance from our Tech Support Team.



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- PKI Support

 10/20/2020 4:23 AM
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jieun

Posts: 4
Joined: 10/20/2020

thanks for reply.

Then, I also question about how can I SEE the atom type of molecule that I draw in the chem3d program.

 10/29/2020 3:30 AM
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CS RNA

Posts: 683
Joined: 2/25/2009

While placing the mouse pointer over the atom you will get the atom type inforamtion.

You will get the basic information from the Chem3D Help menu as well as in the manual.



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- PKI Support

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