[gmx-users] not integer charge

Justin Lemkul jalemkul at vt.edu
Tue Jan 8 11:55:44 CET 2013

On 1/8/13 3:00 AM, sara azhari wrote:
>   Hi all,
> I have not integer charge in my system (-0.11). I want to neutralize this charge by adding Na+. but I don't know how do this. I have an amino acid only in a box . adding one Na+ is wrong. because in pr step, system gives error and wrote odb file for each step. please guide me.

Your topology is wrong.  You probably chose incorrect termini when running 
pdb2gmx.  If you have a single amino acid, you need to choose zwitterionic 
termini, if applicable.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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