Regarding system construction and specific flags for membrane simulations, there are some details here:
https://github.com/callumjd/AMBER-Membrane_protein_tutorial
Best,
Callum
-----Original Message-----
From: King Wu <lodking407.gmail.com>
Sent: Wednesday, December 1, 2021 1:22 PM
To: daniel.r.roe.gmail.com
Cc: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Equilibrate and Production Run Membrane-protein complex
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Thank you, I have tried using CHARMM-GUI and it works very well.
On Wed, Dec 1, 2021 at 5:46 AM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> 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:
> https://urldefense.com/v3/__https://aip.scitation.org/doi/abs/10.1063/
> 5.0013849__;!!N3hqHg43uw!_iE8dbW3B6cCELza0PdiGd3dTs1jKytVES5iNCwV0qP-i
> Fg9bZmm5nlf8SHRPevzkDf5yw$
>
> I've implemented it in an Amber-specific script here:
> https://urldefense.com/v3/__https://github.com/drroe/AmberMdPrep__;!!N
> 3hqHg43uw!_iE8dbW3B6cCELza0PdiGd3dTs1jKytVES5iNCwV0qP-iFg9bZmm5nlf8SHR
> Pevl2uHU0Q$
>
> Hope this helps,
>
> -Dan
>
> On Wed, Nov 24, 2021 at 8:16 PM King Wu <lodking407.gmail.com> 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 - 12:00:03 PST
