On Thu, May 19, 2011 at 8:20 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?
>
My suggestion would simply be to run MD with weak restraints on the protein
system and let the waters diffuse in there naturally (in an NTP ensemble).
To me, this is a better solution to "guessing" where the waters would go.
HTH,
Jason
>
> 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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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu May 19 2011 - 05:30:05 PDT
