[gmx-users] Aquaporin in DOPC

[Justin Lemkul]

On 1/27/14, 4:02 AM, jhosamelly wrote:
> I was able to do the KALP-15 in DPPC. Thanks to the tutorial by Justin
> Lemkul.
> Now, I tried to do it with a different protein and lipid.
> I used aquaporin (protein) and DOPC (lipid)
> I now have the solvated Aquaporin in DOPC.
> Now, I'm wondering, should I put ions too? to neutralize the system? If yes,
> what ion and what charge should I put in my system?

Do you know which algorithms require charge neutrality, and are they relevant to 
you?  Which ions make the most sense given what you want to model?  NaCl is the 
most common salt used in most simulations, but you should consider what it is 
you're trying to model and what concentration might be relevant.

> I tried to search online I can't see what charge aquaporin has.
>

Because such information doesn't exist, because charge is not an intrinsic 
property of a protein; it is a function of the environment.  You may be able to 
find a pI value, but the charge the protein bears depends on how you treat it. 
The total charge of your protein, as determined by the choices you make during 
pdb2gmx, is stored in the topology.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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