[gmx-users] Adding charges to a protein to observe interaction

[Justin Lemkul]

On 8/5/13 10:19 AM, chinnu657 wrote:
> Hi,
>
> I have a box with 2 proteins in them. I want to add charges to each of the
> protein so that I can
> observe how the respective protein interacts with their respective charge
> cloud. The proteins I'm using are 2CDS.pdb and 1AKI.pdb from the RCSB bank.
>>
>
>>From what I figured, I tried using genion under the impression that I could
> replace the solvent molecules with CL ions but I don't think this worked.
>
> I'll really appreciate some help on this.
>

The only way to "add charges" to a protein is to reconstruct a topology and 
configuration that has a different protonation state.  pdb2gmx allows you to do 
this by interactively selecting the protonation state for any of the titratable 
amino acids.

-Justin

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

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

==================================================