[gmx-users] Amber&Buckingham

Justin Lemkul jalemkul at vt.edu
Sun Apr 21 23:56:10 CEST 2013

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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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