[gmx-users] interaction force between Mg and Oxygens of phosphate, in CHARM36 force field

[Justin Lemkul]

On 1/20/18 2:42 AM, Sajad Ahrari wrote:
> Hello Dears,
> I am using CHARM-36.ff for my simulation. I have Mg ions and ATP as hetero-atoms in my system (the Mg-ATP complex). I am trying to know about the amount of interaction force between Mg ions and phosphates of ATP that is already set in this force field. Could you please help me know if I can find about these parameters in the force field files?

The force field files define the parameters for the different 
interactions. You can compute a LJ interaction energy using normal 
combination rules and some input distance. The same with the 
electrostatic interaction; apply Coulomb's Law. The .rtp file has the 
charges in that case, and LJ are in ffnonbonded.itp.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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