[gmx-users] simulation of a protein including calcium ion

[Justin A. Lemkul]

leila karami wrote:
> Dear Justin
> 
> thanks for your attention
> 
> in my case calcium ion is bonded to 4 oxygen atoms of C=O group of 
> protein. yes, Calcium ions are present in nearly all the force fields in 
> Gromacs. but there are only parameters in * nb.itp and not in * bon.itp. 
> how to obtain these new parameters for my case?
> 
> 

Deriving new bonded parameters is not a simple task, and may or may not be 
appropriate.  A coordination complex may be held in place by electrostatic 
interactions, or you may choose to use distance restraints to keep the bonded 
geometry in place.  If you think that actual (chemical) bonds should be present, 
then there is not a suitable force field for you to use, since the charge 
transfer effects will invalidate the charges assigned to C=O groups by the force 
field.

-Justin

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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