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
--
========================================
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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