AMBER Archive (2008)

Subject: AMBER: atom type for carbon and nitrogen atoms

From: Catein Catherine (askamber23_at_hotmail.com)
Date: Mon Oct 27 2008 - 03:56:06 CDT

Dear Sir/Madam,
 
I am interested do MD stimulations for an inorganic compound. This inorganic compound bind with isocyanide, i.e. transition metal-C(triple bond)N-(tert-Bu).
 
I defined the atom types for the transitional metal and the tert-Butane. However, I found atom type for C(triple bond)N cannot be defined. I run the min and md calculations by defining C and N as C2/N2 or C3/N3. The minimization finished normally, but the md simulations clash everytime.
 
While chemical instutation tell me that transitional metal -C(triple bond)N-Carbon should be linear, the md start to change the angle and dihedral angles automatically. I think it is because I did not define the isocyanide C atom and N atom correctly. Could anyone give me a hand to teach me how to solve this problem?
 
patd.
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