Hello,
I have performed TI for mutating TYR->PHE in a system two different ways:
1) AMBER 9, using dummy atoms to balance topology files, 2-step TI
(mutate charges, then mutate vdW)
2) AMBER 10, no dummy atoms, 3-step TI (remove charges, vdW
transition, add charges)
For the first way, the charge mutation, or electrostatics contribution
was calculated to be: 23.84.
For the second way, the charge removal contribution was calculated to
be 31.15, and the charge addition contribution was calculated to be
6.82 for a sum of 37.91.
So the electrostatics contributions calculated using different methods
are different, unless I am mistaken and should subtract the charge
addition contribution from the charge removal contribution in the
3-step method, which would give me approximately the same answer as
the 2-step method. 23.84 ~ 24.33. Is this the correct solution to this
discrepancy, or have I made a mistake somewhere in my calculations?
Also, why is it that softcore potentials used for the vdW transition
in the AMBER 10 3-step TI method cannot use clambda values <0.01 or
>0.99? This prevents the use of 12-point gaussian quadrature because
the 1st and 12th quadrature points fall outside of the allowed range.
Thanks for any clarification,
-Jodi
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Received on Mon Jul 06 2009 - 11:04:05 PDT
