I believe that leap works the way you suggested. The problem for
smallcavities is that you need near perfect overlap with a water in your box
for it to be retained.
On May 19, 2011 8:21 AM, "Sindrila Dutta banik" <
sindrila.duttabanik.yahoo.com> wrote:
Thanks for the reply. When using Leap (explicit solvent model), the solvents
are located surrounding the protein and not WITHIN the cavities of protein
(not as internal water molecules). In case, when a protein is immeresed in a
box of water, water is expected to be present in the cavities within protein
structure. How to get that?
From: Carlos Simmerling <carlos.simmerling.gmail.com>
To: Sindrila Dutta banik <sindrila.duttabanik.yahoo.com>; AMBER Mailing List
<amber.ambermd.org>
Sent: Thursday, 19 May 2011 6:06 PM
Subject: Re: [AMBER] Solvation
How is this different from what Leap does? Please be more specific.
On May 19, 2011 8:02 AM, "Sind...
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Received on Thu May 19 2011 - 06:00:02 PDT
