[gmx-users] not integer charge
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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users