[gmx-users] Amber&Buckingham

[Justin Lemkul]

On 4/21/13 1:53 PM, Ali Alizadeh wrote:
> Dear All users
>
> I want to use amber ff and there are some particles(mineral and
> organic) in my system that
>
> non bonded interaction between them is buckingham,
>
> Is it possible to simulate this system in gromacs?
>

You cannot mix LJ and Buckingham interactions.

> There are some alkane molecules such as decane but I did many search
> and studied all of the
>
> paper that are were related to amber but I could not find the partial
> charge of atoms in amber
>
> force field and for decane,
>
> How can I find the partial charge of atoms in decane?
>

Surely in your reading you came across GAFF and specific methodology for charge 
calculations, no?  If not, there is a lot out there to tell you how to do the 
necessary calculations.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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