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

[Justin Lemkul]

On 6/1/15 10:18 AM, MPI wrote:
> Hi Justin,
>
>     Thank you very much for your suggestion. Please see below.
>
> Thanks,
> Dewey
>
>>> 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.
>
>       If choosing (2), what is the concern ?
> Why adding NH3 as part of water_and_ions after protein-lipid  is
> equilibrated already ?
> Choosing (2), I have to go through equilibration twice.
>

No you don't.  You add NH3 into the box, then solvate with water.  See 
http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents

I'm saying that (2) is in general more logical for your purpose (as I understand 
it) but you don't do two separate equilibrations.  Moreover, it is unlikely that 
you'll be able to find space in an equilibrated layer of water to insert NH3 
molecules.

> Also,  if the substrate is a very small ligand, is the protocol the
> same ?  Namely, adding a new substrate AFTER protein-lipid is
> equilibrated.  Then perform another equilibration for the substrate +
> protein-lipid.
>

This is context-dependent.  If you want to simulate a protein-ligand complex in 
a bilayer, you add the ligand first into the protein (crystal structure, 
docking, etc).  If you want to observe partitioning from bulk solvent of the 
ligand into the protein's binding site, then it's the same.  Put the required 
number of ligands into the box where the solvent will be, then add the solvent 
(water).

>
>
>>> Also,  if the substrate has a charge, which order is preferred ?
>
>
>> Charge shouldn't affect the protocol.
>
> Did you mean  when adding a new substrate, eg, NH4+ or Ca2+  into a
> protein-lipid system,  one has to remove all ions  and water in the
> equilibrated protein-lipid system,  put back ions and water again and
> finally equilibrate the new system right after ?
>

Or just build it in sequence from scratch without having to remove water and 
ions.  That's what I'm suggesting above.  The cosolvent/ligand/whatever is 
always added before the water.  It's easier and faster in practical terms, 
because if you have to remove solvent, then what was the point of the initial 
equilibration?

-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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