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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Received on Sun Oct 22 2006 - 06:07:37 PDT
