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 PEO.in
> 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.top peoli.crd
Bill Ross
Received on Thu Jul 08 1999 - 17:39:38 PDT
