[AMBER] Equilibrate and Production Run Membrane-protein complex

From: King Wu <lodking407.gmail.com>
Date: Wed, 24 Nov 2021 17:15:40 -0800

Hi, Amber

I have used VMD to build a membrane-protein complex with water layer and
ion concentration. files are outputted as psf and pdb, and should be ready
to use in AMBER. I wonder if there is a protocol I can follow to
equilibrate my system and perform a 20ns production run? steps like TLEAP,
solvate water box and minimization before equilibration and production?

Any precaution I should pay attention to?
1, for example, the periodic boundary in the c cell? (I am asking because
in the c cell, I am not sure what size I should use as partial protein is
not covered by the lipid layer. Should I leave the partial protein region
overlapping with its periodic boundary? It is easy to work on the a and b
cells as it would need ~1 to 2 A for gapping and can be seen from VMD, but
I am not sure how to determine the c cell in terms of the periodicity).
2, how to determine and how to select which atoms/region I should fix when
running equilibrium and production?
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Received on Wed Nov 24 2021 - 17:30:03 PST
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