[gmx-users] charge neutralization in vacuum simulations

tasneem kausar tasneemkausar12 at gmail.com
Tue Sep 1 11:57:11 CEST 2015

Dear Gromacs users

I am trying to neutralized the protein having two chains with four negative
I ran the command line as : pdb2gmx -c prtn.pdb -p -o -glu -asp.
I have  chosen one protonated glu and one protonated asp for each protein
The net charge is now zero.
Am I going through the right step for the neutralization?
If there is any other way to neutralize protein, please suggest.

Thanks in advance

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