VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Jul 11 2006 - 23:45:30 CDT

Dear Harish,
you can find topologies for all of the ions currently used by autoionize
in ions.top, in the plugin directory. If you add a bicarbonate topology
entry here, you should be able to use bicarbonate as well (you just need
to create a normal charmm topology entry for a bicarbonate residue).
This also means that you need to change the piece of code under the
comment "make topology entries" to use your bicarbonate residue name
instead of CLA.
If you want to use divalent cations, things work normally if you specify
the ion number, but you need to change the ion number calculation code
(after the comment "compue Nna and Ncl") to halve the number of
whichever is the divalent ion in your system.

In the new future autoionize will hopefully be much more versatile and
easier to adapt for this sort of thing, but this is the set of changes
you'd need to make to have this working right now.

Peter

hl332_at_drexel.edu wrote:
> Hi all,
> I want to add ions in my system other than sodium and pottasium as given in autoionize plugin manual. It (explicitly TCL SCRIPT) also says how to change different ions but i dont know what to do if i want to add HCO3-(bicarbonate ions) and moreover at a later stage if i want to add divalent ions. please help!!!
> Regards and thanks in advance...
> Harish...
> -------------------------------------------------
> Harish Vashisth
> Graduate Student(Ph.D)
> CAT-361,Department of Chemical & Biological Engg.
> Drexel University, Philadelphia, PA
> office: 215-895-5823
>