AMBER Archive (2004)

Subject: AMBER: which parameters for Ca2+ ?

From: cailliez (
Date: Tue Apr 06 2004 - 02:50:03 CDT

Dear Amber users,

I have a question about parameters for Ca2+ cations. I want to run a
of a protein with and without calcium ions to study the influence of
this ion on the
dynamics of my protein (I would like to use parm99).
I saw different parameters for it :
- in parm91.dat : r0=1.60A, and E=0.1kcal/mol
- in parm99.dat : r0=1.7131A and E=0.459789kcal/mol
- in : r0=1.7900A and

All these numbers are really different and I do not know which one I
should use.
I guess I should use those from parm99 as I want to use these parameters

for other variables but I am not sure,
and maybe one of you has an idea on this subject.
I understand this is a big problem since I read somewhere in the archive

that divalent cations are not
a common feature of molecular mechanics.

Thank you in advance for all your suggestions,

Fabien Cailliez                         Tel : 01 58 41 51 63
Laboratoire de Biochimie Théorique      e-mail :
IBPC    13, rue Pierre et Marie Curie
75005 Paris

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