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
--
========================================
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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