[gmx-users] adding molecules - doubt

[Osmair Vital de Oliveira]

Hi Fernando

Using:
genbox -cp minimized_box.gro -ci spc216.gro -o
minimized_water3.gro -p aki.top

use too: -box x y z

Osmair V. Oliveira
UFSCar - SP - Brazil

On Tue, 8 Nov 2005, Fernando Mattio wrote:

> Hi Dallas and gromacs users,
> I understood what you wrote, but I had problems...
> I have a protein in a box, and also one file (spc216.gro) with 256 water
> molecules coordenates, and of course the spc.itp file. I am trying to learn
> how to add exactly these 256 molecules with it´s coordenates in the box...
> I tried: genbox -cp minimized_box.gro -ci spc216.gro -nmol 256 -o
> minimized_water3.gro -p aki.top
> But I got the Fatal Error: more than 1 residue in insert molecules. Program
> terminated.
> I couldn´t understand this error.
>
> I tried also : genbox -cp minimized_box.gro -ci spc216.gro -o
> minimized_water3.gro -p aki.top
> And only 78 water molecules were added.
>
> I also read in the manual that "At the moment -ci only works when inserting
> 1 molecule". What does it means, that I should add one by one the 256
> molecules?
> Or shouldn´t I use genbox (and maybe work with the topologies files) for
> such a thing?
> Many thanks and best regards,
> Fernando Mattio.
>
>
> 2005/11/8, Dallas B. Warren <Dallas.Warren at vcp.monash.edu.au>:
> >
> > Because using the -cs switch tells it to fill the box up with as many of
> > those molecules as it can.
> >
> > If you just want to add a limited number, you need to use the -ci switch
> > with -nmol
> >
> > Catch ya,
> >
> > Dr. Dallas Warren
> > Lecturer
> > Department of Pharmaceutical Biology and Pharmacology
> > Victorian College of Pharmacy, Monash University
> > 381 Royal Parade, Parkville VIC 3010
> > dallas.warren at vcp.monash.edu.au
> > +61 3 9903 9073
> > ---------------------------------
> > When the only tool you own is a hammer, every problem begins to resemble
> > a nail.
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