Re: [AMBER] Equilibrate and Production Run Membrane-protein complex

From: Daniel Roe <>
Date: Wed, 1 Dec 2021 08:46:36 -0500


I'll leave the questions for how to properly buildi the membrane
system to those far more knowledgeable than I (although people have
had lots of success with CHARMM-GUI, you may want to try that).

As far as relaxation of the system, once you've got a
topology/coordinate file you can try to use the following protocol:

I've implemented it in an Amber-specific script here:

Hope this helps,


On Wed, Nov 24, 2021 at 8:16 PM King Wu <> wrote:
> 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 Dec 01 2021 - 06:00:03 PST
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