On Wed, 5 Apr 2017 13:32:05 +0200
Karolina Mitusińska (Markowska) <markowska.kar.gmail.com> wrote:
> 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?
Yes, but with the caveat mentioned below. The question still is: what
problem are you hoping to solve with your approach? Why does pmemd
need to know there are different groups of water? There may be a
better, simpler solution.
> 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.
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Apr 05 2017 - 05:00:03 PDT
