AMBER Archive (2008)

Subject: Re: AMBER: atom type for carbon and nitrogen atoms

From: Gustavo Seabra (gustavo.seabra_at_gmail.com)
Date: Mon Oct 27 2008 - 12:28:31 CDT

On Mon, Oct 27, 2008 at 4:56 AM, Catein Catherine wrote:
> 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.

How are you doing this parametrization? This sounds just like an 'sp'
carbon, no? This is available in gaff. Look for "c1" atom type here:

http://ambermd.org/antechamber/gaff.html#atomtype

HTH, 

-- 
Gustavo Seabra
Postdoctoral Associate
Quantum Theory Project - University of Florida
Gainesville - Florida - USA
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