VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Jul 12 2006 - 01:57:31 CDT

(To elaborate on this, you're also going to need to change the "CLA" in
the coord statements under "assign ion coordinates" to the name of one
of the atoms from your bicarbonate residues, and then add a guesscoord
statement later to get the remaining coordinates. This is going to give
you an array of identically oriented bicarbonate, so some extra
equilibration may be required)

Peter Freddolino wrote:
> 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
>>