Hi Dr Steinbrecher,
I'm interested in calculating the hydration free energies of dummy/neutral
atom to K+ in water and dummy/neutral atom to Cl- in water using AMBER 11.
These are two different transformations and later I want to do a double
mutation of neutral atoms to K+ and Cl- and get the hydration free energies
of the salt.
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.
Sorry if this question has been posted/answered already.
Regards
Sai
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Received on Tue Jan 03 2012 - 12:00:02 PST
