Ok, so I'll try with the topology file.
Thank you very much!
Have a nice day
Karolina
2017-04-05 14:42 GMT+02:00 Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk>:
> 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
> > >
> > >
> > > _______________________________________________
> > > 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
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Apr 05 2017 - 06:00:11 PDT
