<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
On 13/09/2011 12:03 AM, m r wrote:
<blockquote
cite="mid:1315836199.27921.YahooMailNeo@web34507.mail.mud.yahoo.com"
type="cite">
<div style="color: rgb(0, 0, 0); background-color: rgb(255, 255,
255); font-family: times new roman,new york,times,serif;
font-size: 14pt;">
<div style="RIGHT: auto"> Dear all,</div>
<div style="RIGHT: auto"> </div>
<div style="RIGHT: auto">In an attempt to simulate the effect of
adding calcium ion to the solvent</div>
<div style="RIGHT: auto">around my protein of interest, I wonder
how to add Ca2+ ions in the </div>
<div style="RIGHT: auto">following cases (in GROMACS 4.5.4):</div>
<div style="RIGHT: auto"> </div>
<div style="RIGHT: auto">1) adding Ca2+ ions randomly
distributed in the solvent;</div>
</div>
</blockquote>
<br>
genion does this<br>
<br>
<blockquote
cite="mid:1315836199.27921.YahooMailNeo@web34507.mail.mud.yahoo.com"
type="cite">
<div style="color: rgb(0, 0, 0); background-color: rgb(255, 255,
255); font-family: times new roman,new york,times,serif;
font-size: 14pt;">
<div style="RIGHT: auto"> </div>
<div style="RIGHT: auto">2) adding Ca2+ such that it is
initially restrained in vicinity of some </div>
<div style="RIGHT: auto">specified groups on the surface of my
protein (I mean: something similar to</div>
<div style="RIGHT: auto">restraining the ligand in a search box
during its docking to a receptor).</div>
</div>
</blockquote>
<br>
Nothing in GROMACS does this.<br>
<br>
Mark<br>
</body>
</html>