Your problem is the analysis with your own code, not pmemd. If you
can't make your software more flexible then I would suggest to use a
separate topology file with altered residue names solely for the
purpose of analysis with that program.
On Wed, 5 Apr 2017 14:11:07 +0200
Karolina Mitusińska (Markowska) <markowska.kar.gmail.com> wrote:
> Ok, so here's the thing:
> my research group have developed a software to track water molecules
> during MD simulations. Right now we are working on a feature that
> will allow us to track different kind of molecules during one
> analysis. So I thought it will be great to test it using different
> names for 'different kinds' of water molecules - for example CRY for
> waters from the crystallographic model and WAT for others.
> So, yes, I could note the residue number, but it will be easier for
> me to have CRY and WAT water molecules to track them with our soft.
> Can I make pmemd run this kind of simulation?
>
> Best regards,
> Karolina
>
> 2017-04-05 13:55 GMT+02:00 David A Case <david.case.rutgers.edu>:
>
> > On Wed, Apr 05, 2017, Karolina Mitusińska (Markowska) wrote:
> > >
> > > 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.
> >
> > Just to restate what Hannes said, in different words: just note
> > down the residue numbers that correspond to the "crystal" waters,
> > and use residue numbers rather than names to follow their behavior
> > during a simulation.
> >
> > ....good luck...dac
> >
> >
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Received on Wed Apr 05 2017 - 06:00:08 PDT
