Dear Amber users,
I have a question about parameters for Ca2+ cations. I want to run a
simulation
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
http://pharmacy.man.ac.uk/amber/ion/metals.dat : r0=1.7900A and
E=0.0140kcal/mol
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
--
__________________________________________________________________
Fabien Cailliez Tel : 01 58 41 51 63
Laboratoire de Biochimie Théorique e-mail : cailliez.ibpc.fr
IBPC 13, rue Pierre et Marie Curie
75005 Paris
__________________________________________________________________
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Received on Tue Apr 06 2004 - 09:53:00 PDT
