AMBER Archive (2005)

Subject: Re: AMBER: Amber 8: questions about free energy perturbation

From: David A. Case (case_at_scripps.edu)
Date: Fri Sep 16 2005 - 04:00:13 CDT

On Mon, Sep 12, 2005, Angela Liu wrote:
>
>
> I have read and understood your tutorial of mutating
> toluene to nothing. However, in the Amber 8 manual, it
> specifies that dummy atoms can only exist in the
> perturbed Hamiltonian on Page 134 of Section 5.13:

This restriction will be lifted in the next release. For now, I think you
would have to make the change in two steps, one to remove certain atoms from
one end state, and the other to remove atoms from the other end state (so that
the intermediate state is the same for both cases.) Then you can arrange it
so that dummy atoms are only present in the perturbed state.

...good luck...dave case 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
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