Martini & Gromacs & VMD & Bendix (and ROP)

 Have been playing with the Martini force field for some time now. Still digging. Here is a short movie of a ROP mutant using Martini & Gromacs, and visualized with VMD & Bendix.

Just came out ...

«A molecular dynamics simulation study on the propensity of Asn-Gly-containing heptapeptides towards β-turn structures: Comparison with ab initio quantum mechanical calculations.»

https://doi.org/10.1371/journal.pone.0243429

Molecular simulation of peptides review

Just came out : "Molecular simulation of peptides coming of age: Accurate prediction of folding, dynamics and structures"

http://doi.org/10.1016/j.abb.2019.01.033

αLa : add 15SB to the family

The same image as before, after adding results from the 15SB force field :

A definite improvement over both 12SB and 14SB.

gp41 paper

Just came out : "Folding Molecular Dynamics Simulation of a gp41-Derived Peptide Reconcile Divergent Structure Determinations", ACS Omega, 3, 14746-14754 :

http://doi.org/10.1021/acsomega.8b01579

Just came out :

«Folding Simulations of a Nuclear Receptor Box-Containing Peptide Demonstrate the Structural Persistence of the LxxLL Motif Even in the Absence of Its Cognate Receptor»

http://dx.doi.org/10.1021/acs.jpcb.7b10292

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.

Amber 14SB vs 99SB-STAR-ILDN : αLa peptide

Weblogo representations of secondary structure preferences for human α-Lactalbumin 101-111 peptide with the AMBER ff14SB plus a whole lot of other AMBER force fields. The 14SB simulation was 3 μs, all other 2 μs.

On the way from 12SB to 14SB the α-helical preference was significantly reduced, but the mainly 3₁₀-helical nature of this peptide can not be faithfully reproduced. At least for the time, AMBER99SB-STAR-ILDN still looks like the best force field for this peptide.

Amber99SB-STAR-ILDN : tri-alanine

Added one extra diagram to Figure 3 of this paper. This is a 2.6 μs simulation with a 4 fs timestep (HMR). Nearly identical with AMBER 14SB (?).

New paper from the group just came-out :

Force-field dependent secondary structure preferences

Weblogo representations of the per-residue secondary structure preferences (as produced by STRIDE) for folding simulations of the α-Lactalbumin-derived peptide studied in this paper. Results from seven force fields are shown. The experimental NMR results indicate a mostly 310-helical N-terminal part (residues 3-6) with an occupancy of ~50%, and a completely disordered C-terminus. The symbols in the weblogo diagrams are G => 310 helix, H => α helix, T => turn, C => random coil, E => extended. The force fields are CHARMM22, OPLSaa, AMBER ff12SB, AMBER ff99SB, and three variants of AMBER ff99SB (99SB-ILDN-NMR, 99SB-ILDN, 99SB-STAR-ILDN). It does look like a clear take-home message is present in these diagrams...

Homepage update

Publications and abstracts updated to include latest J. Phys. Chem. B paper