[gmx-users] Force constant, regarding

[RAHUL SURESH]

Sorry for the duplicate post.

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
value.

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
methods?

Sorry I have dumped the mail with too many questions.


On Wed, Sep 12, 2018 at 11:52 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
> value.
>
> 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
> methods?
>
> Sorry I have dumped the mail with too many questions.
>
>
>
> --
> *Regards,*
> *Rahul *
>


-- 
*Regards,*
*Rahul *