Hi,<br><br>Please correct me if I am wrong.<br><br>In that case then, I will have polyhisitine in the box size 12 12 12 and then If I add dhb anions and Li cations, they will be placed randomly in the box.<br><br>When I add then the 1 Li cation, water methanol sphere, how is it necessary it will cover/solvate all the ions that I had added in the box?<br>
Some might still be in open space of the box?<br><br>Thanks,<br>SN<br><br><br><br><br><br><div class="gmail_quote">On Wed, May 25, 2011 at 3:43 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im"><br>
<br>
Justin A. Lemkul wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
<br>
shivangi nangia wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hi Justin,<br>
<br>
Thanks a lot!<br>
Things worked.<br>
<br>
Now I, however, have a different problem in extension to what I am doing.<br>
<br>
I was able to created a sphere of water and methanol around a polypeptide and 1 Li+ ion.<br>
<br>
editconf -f 1li.gro -c -box 12 12 12 -o onlyli.gro<br>
genbox -cp onlyli.gro -cs mix.gro -shell 3 -o li_sol.gro<br>
genbox -cp li_sol.gro -cs mix.gro -shell 3 -o 6nmshell.gro<br>
editconf -f his20.gro -d 0 -o onlyhis.gro<br>
editconf -f onlyhis.gro -c -box 12 12 12 -o hisinbox.gro<br>
genbox -cp hisinbox.gro -cs 6nmshell.gro -o 6sys.gro<br>
<br>
<br>
Now I need to add few more Li ions and anions in the sphere.<br>
<br>
I tried doing that,<br>
genbox -cp 6sys.gro -ci 1dhb.gro -nmol 20 -o added_dhb.gro -p topol.top<br>
<br>
(1dhb.gro is 2,5-dihydrobenzoic acid anion)<br>
<br>
But, since the sphere 6sys.gro is essentially in a box, the dhb anions ...some got randomly placed inside the sphere and some in the open spaces of the box in which 6sys.gro is sitting.<br>
<br>
How can I place all the anions and then Li+ ions specifically inside the sphere?<br>
<br>
</blockquote>
<br>
That's what genion is for.<br>
</blockquote>
<br></div>
I take that back, genion doesn't work for polyatomic ions. The better approach is to construct your system with solute, ions (which in this case are just other molecules floating around), etc, before adding the sphere of solvent.<div>
<div></div><div class="h5"><br>
<br>
-Justin<br>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
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