[gmx-users] genion

Que Pasa quepasa41 at gmail.com
Sat May 24 22:12:43 CEST 2014

If you want a simulation w/o Zinc as a control then build a new system/pdb
w/o it (just delete the Zn line)  rather than doing something exotic like
turning off its charge. Turning off charges (and van der Waals parameters)
is an approach more suitable for alchemical calculations
http://www.alchemistry.org/wiki/Main_Page . Avoid jumping into these unless
you know exactly what you are doing.

On Fri, May 23, 2014 at 12:21 PM, elham tazikeh <elham.tazikeh at gmail.com>wrote:

> dear users
> i studied on amyloid beta peptide with zinc cation and
> i choosed 1ze9 as my pdb file
> can i assume Zn without charge in  protein simulation alone,
> or i have to using the amyloid beta peptide alone as pdb
> for instance,1iyt???
> best wishes
> --
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