AMBER Archive (2006)

Subject: AMBER: single or dual topology for TI?

From: Holly Freedman (freedman_at_phys.ualberta.ca)
Date: Sat Oct 21 2006 - 13:20:51 CDT

Dear AMBER help list,

I plan to use AMBER8 to set up some thermodynamic integration calculations for determining relative
free energies of colchicine (a three-ring, 54 atom organic molecule) and various derivatives in water. I
would like to know if the TI implementation coded in AMBER8 works better for single or
dual topology TI. I am going to set up TI where an OCH3 group (all atom representation) on colchicine
is mutated to an OH group, or as another example, to an OCH2CHCH2 group, and I was wondering if I
should use dual or single topology perturbation. For example in the first case I gave of mutating OCH3
to OH, should I change that C on colchicine into an H and the three H's into dummy atoms, or should I
change all atoms in the CH3 group into dummy atoms and then also have a dummy atom on the
colchicine that I change into an H? I've never done TI before, and it would be great to hear any advice
you have on this.

Thanks,
Holly Freedman 

--
Department of Physics, University of Alberta
Edmonton CANADA
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