[gmx-users] adding molecules - doubt

Fernando Mattio mattiofer at gmail.com
Tue Nov 8 10:27:52 CET 2005

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
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
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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