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, "Sindrila Dutta banik" <
sindrila.duttabanik.yahoo.com> wrote:
Hello!!
Is it possible to overlay a protein structure on a large box of bulk water
and followed by deleting water that overlap with protein by AMBER11, as in
the following Ref.
Proteins: Structure, Function and Genetics, 1998, 32, 362-380 (the ref. is
enclosed plz. find it)
How to do this? Please let me know.
Sindrila Dutta Banik
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Received on Thu May 19 2011 - 05:30:04 PDT
