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On 10/01/2012 10:46 PM, Steven Neumann wrote:
<blockquote
cite="mid:CAKZJqQE+H-NcqKTaY_pbRNvJb5zaEAvLiAY-U4cSYabx6UZgDA@mail.gmail.com"
type="cite">Thank you. Imagine I would like to put ligands in
further simulations. Should I then copy coordinates of my ligands
in smaller box (not to overlap my tube) and then copy both
coordinates of ions and ligands plus protein?<br>
</blockquote>
<br>
Any way you want to construct your non-overlapping non-solvent
non-ion molecules is fine. Previous EM of each is wise, but not
necessarily required - vacuo EM is probably fine. Then solvate, then
use genion, then EM the whole system. Copying ions from earlier
calculations is a good way to generate atomic clashes, which is a
high price to pay for randomly-placed ions that are different from
those generated as above.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAKZJqQE+H-NcqKTaY_pbRNvJb5zaEAvLiAY-U4cSYabx6UZgDA@mail.gmail.com"
type="cite">
<br>
<div class="gmail_quote">On Tue, Jan 10, 2012 at 11:31 AM, Mark
Abraham <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span>
wrote:<br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px
0.8ex;PADDING-LEFT:1ex" class="gmail_quote">
<div class="im">On 10/01/2012 10:13 PM, Steven Neumann wrote:<br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px
0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote">Thank you.
Should I also copy and paste coordinates of my ions or
just my protein?<br>
<br>
</blockquote>
<br>
</div>
The randomly-placed ions will be immaterial for EM.
<div class="HOEnZb">
<div class="h5"><br>
<br>
Mark<br>
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