AMBER Archive (1999)

Subject: about setting up INITIAL STATE containing dummy atoms in FEP calc

From: yongping pan (panyp_at_u.washington.edu)
Date: Sun Nov 14 1999 - 22:56:44 CST

 Hi,
 I have trouble in using dual topology technique to carry out FEP/MD calc.
 That is, to mutate some real atoms to dummy ones and to mutate some dummy
 atomes to real atomes in a single run. In the manual it is mentioned that
 these dummy atomes in the initial state has to be included in the residue
 that needs to be mutated. But it doesn't explain how to do it and there
 is no demo for this kind of mutation. So my question is:
 
 (1). Do I need to define a new residue so that these special dummy atoms
 can be properly treated by the edit module? Otherwise, how can I make
"edit" program to keep those dummy atoms?
 
 (2). In the case like mutation from ALA to PHE, the mapping of the
 topology between initial and final states seems relatively easy for me.
 But what about the mutation from ARG to PHE? If I want to mutate one of
 the hydrogen that is attached to the terminal nitrogen to Carbon, and I
 hope this Carbon form a colvalent bond with the GAMA Carbon, how can this
 be done?
 
 Thank you very much for taking care of my problems.
 
 **************************************
 Pan, Yongping
 Department of Medicinal Chemistry
 University of Washington
 Seattle, WA 98195
 
 panyp_at_u.washington.edu
 (206) 685-1000
 (206) 685-3252 (fax)
 http://faculty.washington.edu/~panyp
 **************************************