[AMBER] enhanced sampling conformations by AMD

From: Kat G <katwin86.gmail.com>
Date: Mon, 7 Nov 2016 11:03:29 -0600

Hi all,

I am using AMD to explore protein conformations (630 residues) in the
presence and absence of ligand. I used info from CMD at 10ns to calculate
Ethres and alpha for potential and dihedral from Amber manual. After
running 30ns of AMD, the backbone RMSD keeps increasing up to 15A. The
boost energies for potential and dihedral are reported around 1200 and
40kcal/mol respectively. Protein structures from AMD trajectories fluctuate
strongly and seem to be distorted.

Does that mean the boost energy is too high? How can I know my trial
parameters for AMD work or not (not too high or low boost). And what kind
of analysis should I try to make sure the enhanced sampling structures are
acceptable to continue with cluster analysis to finally answer for the
differences between protein conformations with and without ligand.

Could you please give me any suggestion. Thanks
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Received on Mon Nov 07 2016 - 09:30:03 PST
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