[gmx-users] Adding a substrate into protein-lipid bilayer system

[Justin Lemkul]

On 5/31/15 4:17 PM, MPI wrote:
>   Dear Users,
>
>      I have a protein-lipid bilayer system and this protein is an ion
> channel.  I would like to force a substrate eg, ammonia (NH3) passing
> through this channel.
>
> I wonder when it is appropriate to add NH3 into the system and how to
> setup the control of temperature coupling in thermostats.
> For example,
>
> 1.  add NH3 first with the protein and  then embed protein-NH3  into the lipid
>
> or
>
> 2.  embed the protein into  lipid with an equilibration,  followed by
> adding NH3 into the system
>

If you want NH3 to pass through the channel, I'd say (2), more or less, but 
really you should add NH3 as a cosolvent as part of the equilibration.  Add the 
NH3 in the box, add water, and equilibrate.

>
> Also,  if the substrate has a charge, which order is preferred ?
>

Charge shouldn't affect the protocol.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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