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.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Apr 05 2017 - 03:00:02 PDT
