[gmx-users] Re: topology and coordinate file not matching after grompp

Justin Lemkul jalemkul at vt.edu
Mon Aug 5 13:47:40 CEST 2013

On 8/5/13 5:39 AM, chinnu657 wrote:
> Hi Justin,
> The simulation is running fine for this task. Thank you for helping me
> There's something additional I want to do and I'd like to know how you'd
> approach it. 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 im 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'd really appreciate it if you could share your thoughts on this

I don't see how adding ions into the solvent would help you understand anything 
about changing charges on the protein.

Please start a new thread if you're introducing a new topic for discussion.



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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