AMBER Archive (2008)

Subject: AMBER: Silicon parameters

From: Abdul Hameed, MohamedDiwanMo (mabdu3_at_email.uky.edu)
Date: Wed Aug 20 2008 - 11:15:56 CDT

Dear Amber Users,
I am interested in doing MD for a small molecule ligand with silicon atom. I am studying the binding mode of the small molecule with the protein active site. Unfortunately, I could not find the parameters for silicon.

I searched the archive and noticed that many other people inquired the same but got no answers. And the other alternative suggested by Scott is to use the c3 gaff values (as a last resort). It will be very helpful if someone can help me regarding the parameters for Silicon related bonds, angles and dihedral angles. If you can point to any references, suggestions, links or publications it will be very useful.

Thanks in advance.
Regards,
Diwan

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