[gmx-users] calcium parameters

Mahnam mahnam at ibb.ut.ac.ir
Mon Jul 11 18:30:52 CEST 2011

 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)
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.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110711/f82db3b7/attachment.html>

More information about the gromacs.org_gmx-users mailing list