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://aip.scitation.org/doi/abs/10.1063/5.0013849
>
> I've implemented it in an Amber-specific script here:
> https://github.com/drroe/AmberMdPrep
>
> 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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>
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Received on Wed Dec 01 2021 - 10:30:02 PST
