<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html; charset=UTF-8" http-equiv="Content-Type">
</head>
<body text="#000000" bgcolor="#ffffff">
On 12/07/2011 2:30 AM, Mahnam wrote:
<blockquote cite="mid:WC20110711163052.760075@ibb.ut.ac.ir"
type="cite">
<div><font style="font-size: 10pt;">
<h3 style="color: red;"><br>
<span style="font-size: 18px;"><span style=""><span
style="font-family: Arial;">In God we trust</span></span></span></h3>
</font></div>
<h3 style="color: red;"><span style="font-size: 18px;"><span
style="font-family: Arial;">Hi GMX-users</span></span></h3>
<div><span style="font-size: 18px;"><span style="font-family:
Arial;">I want to do MD simulations of amylase which has 3
ca2+ ions by Gromacs 4.5.3 and charm22 force field.<br>
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)<br>
</span></span></div>
</blockquote>
<br>
Why do you want angle parameters for your Ca2+ ions?<br>
<br>
What makes you think that the chemical behaviour of divalent Ca ion
resembles Ca bound to oxygen?<br>
<br>
Check out <a
href="http://www.gromacs.org/Documentation/How-tos/Parameterization">http://www.gromacs.org/Documentation/How-tos/Parameterization</a><br>
<br>
Mark<br>
<br>
<blockquote cite="mid:WC20110711163052.760075@ibb.ut.ac.ir"
type="cite">
<div><span style="font-size: 18px;"><span style="font-family:
Arial;">
Of course I will correct charge of Ca+2 and its ligands
according to lensink thesis for charge transfer effects.</span></span></div>
<div><span style="font-size: 18px;"><span style="font-family:
Arial;"><br>
Thank you very much in advance.<br>
</span></span></div>
</blockquote>
<br>
</body>
</html>