>To add water molecules, you will have to use tleap to recreate a new
topology file.
Note that (as far as I know), tleap won't read in your prmtop and
rst/inpcrd file, so you need to first write a pdb file of your system (e.g.
with ambpdb or else the trajout functionality in ptraj/cpptraj) and read
that with tleap, add waters and write your new prmtop/inpcrd.
--Marc
On 29 August 2012 05:24, Jason Swails <jason.swails.gmail.com> wrote:
> You can *remove* waters with parmed.py, but not add them.
>
> To add water molecules, you will have to use tleap to recreate a new
> topology file.
>
> HTH,
> Jason
>
> On Wed, Aug 29, 2012 at 12:10 AM, Liu Denis <cndenis.gmail.com> wrote:
>
> > Hi，
> > Use parmed.py in Ambertool.
> >
> > Denis
> >
> > 2012/8/29 Adam Jion <adamjion.yahoo.com>:
> > > Hi all,
> > >
> > > Is there a method that will allow me to add water molecules (or other
> > solute molecules) into a pre-existing topology (.prmtop) and coordinate
> > file (.rst)?
> > >
> > > Regards,
> > > Adam
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> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Wed Aug 29 2012 - 02:00:03 PDT
