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
Mark
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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