[gmx-users] calcium parameters
mahnam at ibb.ut.ac.ir
Mon Jul 11 18:30:52 CEST 2011
In God we trust
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)
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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