Dear All,
In the recent D3R publication by Prof Simmerling, the authors have used $B!H(BFor transition steps involving changing the LJ interactions, the $B&K(B values were set to 0.00922, 0.04794, 0.11505, 0.20634, 0.31608, 0.43738, 0.56262, 0.68392, 0.79366 0.88495, 0.95206,0.99078, 0.995 and 0.999. These exponentially distributed $B&K(B values between 0.00922 and 0.99078, which have more $B&K(B at regions where dU/d$B&K(B changes significantly, as suggested in the Amber manual. Based on our experience, the two extra $B&K(B values, 0.995 and 0.999 can allow the scaled potential function to further approach the true end state.$B!I(B
(Page 7 of Blinded prediction of protein$B!>(Bligand binding affinity using Amber thermodynamic integration
for the 2018 D3R grand challenge 4 Junjie Zou1,2, Chuan Tian1,2, Carlos Simmerling1,2,*)
I could not get the corresponding weights used for the last 2 lambda values. Does the AMBER manual have the weights for 0.995 and 0.999?
Any help will be useful.
Thanks
Regards
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Received on Thu Jan 09 2020 - 12:00:02 PST
