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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==================================================
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