[gmx-users] Force constant, regarding
dallas.warren at monash.edu
Sat Sep 15 04:52:32 CEST 2018
Read the papers for the forcefield, that will tell you how things are
On Sat, 15 Sep. 2018, 2:49 am RAHUL SURESH, <drrahulsuresh at gmail.com> wrote:
> Hi Users
> I am performing a simulation for a bonded metal-protein complex system.
> Here I am aware of adding the essential parameters in ffbonded .itp. The
> force constant value (kb) in the ffbonded.itp file is calculated using
> Gaussian. I would like to clarify the method I have adopted to measure kb
> Here the metal is bonded with three residues of a protein. I have isolated
> the metal-bonded residue and optimized using gaussian calculated the Kb
> value. Now in ffbonded.itp file, I have added Metal and residue atom bond
> length and Kb value obtained from QM results, just like
> CU O 0.20134 507545.
> likewise, I have added all the bonds but kb remain the same.
> Regarding bond angle and dihedral, if the metal is bonded with oxygen of
> two histidines, what should be the nomenclature in naming atoms. Naming can
> be our choice or does it need to follow any protocol?
> How to calculate the cth value for the bond angle?
> How do we determine the coefficients of dihedral?
> Do I make the procedure complicated or can anyone suggest if any better
> Sorry I have dumped the mail with too many questions.
> *Rahul *
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