Thanks Dr Steinbrecher.
Currently I'm doing these calculations as you suggested.
Regards
Sai
On Tue, Jan 3, 2012 at 2:37 PM, <steinbrt.rci.rutgers.edu> wrote:
> Hi,
>
> > When I was going through your tutorial, using softcore potential, you
> dont
> > need to have same number of atoms that are undergoing the transformation.
> > But in my case I have only one atom/ion in the transformation. How can I
> > achieve the transformation of a neutral atom to K+ or Cl-? Should I use
> > dummy atoms instead? If so, can you point me how to use the dummy atoms
> > for
> > the necessary transformation?
> > I did not understand how to use/include dummy atoms using ff99SB force
> > field.
>
> Hi,
>
> there is no need to use dummy atoms in the type of calculation you plan.
> Just set up your system as:
>
> System 1 System 2
> Ion + Water just Water
>
> and set scmask in our input files to the Ion residue(s). Make sure all
> water molecules have the same coordinates in Systems 1 and 2 or your sim
> will halt with an error.
>
> This decouples both the (in this case very dominant) Coulomb as well as
> vdW interactions and gives you (with some caveats) the free energy of
> solvation.
>
> Check out the Steinbrecher, Joung and Case J. Comp. Chem. paper for an
> example using Cl-.
>
> Kind Regards,
>
> Thomas
>
> Dr. Thomas Steinbrecher
> formerly at the
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
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Received on Wed Jan 04 2012 - 12:30:03 PST
