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.tazi...@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 > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
