Tuesday, November 28, 2017

Amber 14SB vs 99SB-STAR-ILDN [2]

Have been looking for a mostly disordered peptide (with NMR data available) for which the two force fields would demonstrate detectably different secondary structure preferences. I think I found one :

The upper graph is from 99SB-STAR-ILDN, the lower from 14SB. The two simulations were 24 μs each, both using adaptive tempering (280K-380K). Comparison between observed and calculated  NOEs plus chemical shifts should suffice. Given that this is a mostly disordered peptide ,we should probably also compare the computationally expected vs experimentally observed number of NOEs.

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