> I saw that Amber10
> handles TI better than Amber9 (no need to dummy atoms, etc), but
> currently, we only Amber9 license here.
Why do you think AMBER ver.10 handles TI better than AMBER ver.9? If you
need soft-core potential to do the transformations, that code is written
in ver.10. But if you do not need to vanish the atoms (and use dummy
atoms), the TI code in ver. 9 does a good job. Check out the following
paper, which uses a new mixing function in TI method (implemented in
ver. 9) to do the alchemical transformations from one state another.
"Effects of Restrained Sampling Space and Non-planar Amino Groups on Free
Energy Predictions for RNA with Imino and Sheared Tandem GA Base Pairs
Flanked by GC, CG, iGiC or iCiG Base Pairs" I. Yildirim, H. Stern, J.
Sponer, N. Spackova, and D.H. Turner, J. Chem. Theory and Computation, 5,
2088-2100 (2009).
Ilyas Yildirim, Ph.D.
University of Rochester
Department of Chemistry
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Received on Mon Sep 14 2009 - 13:35:42 PDT
