[gmx-users] adding molecules - doubt

[Viswanadham Sridhara]

Hi Fernando,
How big is your system or say the box size. How big is your protein?
And is there any reason, why you want to add only 216 water molecules?

if you use -ci option, make sure you have only one molecule in
water.grofile and use -nmol xxx to add xxx no. of water molecules, but
if you use -cs
option, the number of water molecules added depends on the box size as well
as the protein inside the box. It adds water molecules to solvate the
protein.

-Viswam.

On 11/8/05, Osmair Vital de Oliveira <osmair at qt.dq.ufscar.br> wrote:
>
>
> 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.
> > > _______________________________________________
> > > gmx-users mailing list
> > > gmx-users at gromacs.org
> > > http://www.gromacs.org/mailman/listinfo/gmx-users
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
>



--
Viswanadham Sridhara,
Graduate Research Assistant,
Old Dominion University, "VIRGINIA".
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20051108/3596433f/attachment.html>