AMBER Archive (2009)

Subject: [AMBER] 2-step vs 3-step TI, and softcores question

From: Jodi Hadden (jodih_at_uga.edu)
Date: Tue Jun 23 2009 - 17:00:02 CDT

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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