Dear all,
I I did MD simulations (500ns) of 15 residues polypeptide and I found, beta hairpin has converted into helix.
My biggest concern is, whether this conversion is MD artefact, means anything simulate for longer time it will convert into any regular structure (whatever i am getting)OR it has biological significance.
another query is I am looking for the best way to represent the transition of beta hairpin to alpha helices (except DSSP). If any body have been through this representation kindly provide me that method.
What force field did you use? Many over-stabilize helices.
DSSP is (in my opinion) by far the best way to represent the structural transition. You can show it in one, clear plot.
Are there any experimental data with which to compare these results, or are the properties of the peptide completely unknown?
If you are worried about force field artifacts, simulate it with a different force field or two, e.g. OPLS and CHARMM.
Experimental data means structural information is available in pdb. which clearly suggest that there is transition between beta-hairpin to alpha helix in same class of protein but different members. this transition is critical for the mechanism.
I will follow your suggestion and run it with OPLS and CHARMM force field.
are these two force fields are more sensitive towards the secondary structure?
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