[gmx-users] calcium parameters

Mark Abraham Mark.Abraham at anu.edu.au
Tue Jul 12 05:24:23 CEST 2011

On 12/07/2011 2:30 AM, Mahnam wrote:
>       In God we trust
>       Hi GMX-users
> I want to do MD simulations of amylase which has 3 ca2+ ions  by 
> Gromacs 4.5.3 and charm22 force field.
> I don’t want to  restraints calcium and I searched mailing list and 
> papers for Ca+2 binding parameters in Charm22 but I only found binding 
> parameters for ca-oxygen (in this paper :New Force Field for Calcium 
> Binding Sites in Annexin–Membrane Complexes) , would you please tell 
> me angle  parameters of Ca-OD1-CG, Ca-O-C, OD2-Ca-O, OD1-Ca-OD1, and 
> dihedral parameters that contains OD1-Ca, Ca-O in middle of dihedral, 
> if it is possible.(OD1= carboxyl, O= carbonyl oxygen)

Why do you want angle parameters for your Ca2+ ions?

What makes you think that the chemical behaviour of divalent Ca ion 
resembles Ca bound to oxygen?

Check out http://www.gromacs.org/Documentation/How-tos/Parameterization


> Of course I will correct charge of Ca+2 and its ligands according to 
> lensink thesis for charge transfer effects.
> Thank you very much in advance.

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