From owner-chemistry@ccl.net Thu Jun 25 22:43:01 2015
From: "sulgi lim sulgi8941]![gmail.com" <owner-chemistry-#-server.ccl.net>
To: CCL
Subject: CCL: add water
Message-Id: <-51470-150625214525-25164-g5clqaosq60yIG7LMfmm8w-#-server.ccl.net>
X-Original-From: sulgi lim <sulgi8941()gmail.com>
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Date: Fri, 26 Jun 2015 10:45:19 +0900
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Sent to CCL by: sulgi lim [sulgi8941/./gmail.com]
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Dear. all users



I have to simulate the membrane system with small molecules..(Those are
non-standard molecules, 32 propofols)
I build DPPC bilayer system, then I have to add water in system by HAND
because my program is AMBER...
However, in leap, I couldn't add water at right position. ("Righg" position
means above and below the lipid-head group of the bilayer, so not iso box)
I tried to add water in tleap like this:

.
.
.
set sys box {60 60 120}
solvatebox sys TIP3PBOX 0.0 iso
.
.
.
After tleap finish, I get the pdb that has a iso box (so, 120x120x120
ang.)..
Therefore, water molecules exist not only outside of lipid-head group but
also side of lipid-tail group.

How can I add water to position that I want ??

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<div dir=3D"ltr"><div>Dear. all users</div><div><br></div><div>=C2=A0</div>=
<div><br></div><div>I have to simulate the membrane system with small molec=
ules..(Those are non-standard molecules, 32 propofols)</div><div>I build DP=
PC bilayer system, then I have to add water in system by HAND because my pr=
ogram is AMBER...</div><div>However, in leap, I couldn&#39;t add water at r=
ight position. (&quot;Righg&quot; position means above and below the lipid-=
head group of the bilayer, so not iso box)</div><div>I tried to add water i=
n tleap like this:</div><div><br></div><div>.</div><div>.</div><div>.</div>=
<div>set sys box {60 60 120}</div><div>solvatebox sys TIP3PBOX 0.0 iso</div=
><div>.</div><div>.<br></div><div>.</div><div>After tleap finish, I get the=
 pdb that has a iso box (so, 120x120x120 ang.)..</div><div>Therefore, water=
 molecules exist not only outside of lipid-head group but also side of lipi=
d-tail group.</div><div><br></div><div>How can I add water to position that=
 I want ??</div><div><br></div><div><br></div></div>

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