Re: charged solute

From: <ross_at_cgl.ucsf.EDU>
Date: Thu 8 Jul 1999 17:39:38 -0700 (PDT)

        I have a box of polymer(PEO) that is well equilibrated. Now, I put
        several Lithium ions in this box randomly and made a PDB file. I am
        ready to run Parm to read force field for Lithium ions and polymer in
        for the MD with Sander.
        I don't know how to put the charge of Lithium ions. I know we put the
        partial charge in Prep input file. Do I have to edit the charge of
        Lithium ions in Prep input file and restart from Prep to Parm ? This
        would be really painful.
        Any pointers will be highly appreciated.
With xleap it would go like this:

> loadamberprep
> x = loadpdb peobox.pdb
> edit x
 [select all atoms by dragging a box, then 'Unit / import unit' to
  bring in a Li+, then move the selected atoms aside so you can see
  the Li+, select it instead, and insert it somewhere.. repeat for
  more Li+] [or you can place it in the pdb using some other graphics
  program that you might like, then 'x = loadpdb' that file.]
 [or, if there are voids where the Li's could fit:
> addions x Li+ <#ions>
> setbox x
> saveamberparm x peoli.crd

Bill Ross
Received on Thu Jul 08 1999 - 17:39:38 PDT
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