Hi,
thanks for your response.
I would like to have two (or more) residues, named for example CRY for
crystal water and WAT for water from the water box, both treated by pmemd
like water residues.
If it is possible, then how to do it?
Best regards,
Karolina
2017-04-05 11:53 GMT+02:00 Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk>:
> On Wed, 5 Apr 2017 11:11:03 +0200
> Karolina Mitusińska (Markowska) <markowska.kar.gmail.com> wrote:
>
> > I would like to distinguish between water molecules from the crystal
> > structure and water molecules of the water box during my simulation.
> > But tleap is changing the names of water residues (both crystal and
> > from the water box) to WAT. And I would like to have two (or maybe
> > even more) 'types' of water molecules residues - from the crystal
> > structure and from the water box.
> >
> > Is there a way to do this?
>
> You would need to be clearer as to why you would want this. At the
> simplest level you could just note the residue and atom indices that
> leap generates in the prmtop file. These numbers are unique and the
> crystal waters will be just the ones with the lowest indices. Maybe the
> adddPDB feature in ParmEd can be useful for annotation of the prmtop
> file.
>
> For MD you may want to be careful with renaming residues because for
> sander/pmemd the name WAT is special (see jfastw flag).
>
>
> Cheers,
> Hannes.
>
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Received on Wed Apr 05 2017 - 05:00:02 PDT
