[gmx-users] not integer charge

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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