[gmx-users] dummies

[Omololu Akin-Ojo]

Hi Maik,

thanks for the response.
To make things clearer:
my pdb file did *not* contain the dummies, but only
the real atoms. if you download a *.pdb file from the
pdb, it does not conatin dummy atoms.
my force field for the non-bonded interaction uses
dummies. My molecule definition (*.itp) also contains
the dummies.
i was hoping i would not have to manually put the
dummy atoms in the *.pdb file. Afterall, from the
molecule definition it is possible to generate the
posions of the dummies. i already did it manually any
way.

someone helped me to customize the gurgle.dat file --
ngmx does not work with the new gurgle.dat but i have
vmd and rasmol to visualize anyway.
i agree they are just quotes, but i don't appreciate
the 'f' word, for example on my computer. i'm not
saying to turn it off for all users, but i just wanted
mine off.

Cheers,
o.

--- Maik Goette <mgoette at mpi-bpc.mpg.de> wrote:

> 1)
> I don't understand your question, it seems.
> If your forcefield-files contain dummy atoms, the
> topology file still 
> doesn't. And thats also true for the gro-file.
> If you want to use dummies, they have to be included
> in the pdb-file, or 
> you have to add them manually in the gro-file and
> the topology later.
> GROMACS is a really fine tool, but the
> "Do-whatever-I-mean"-function 
> isn't included yet...
> The way to use GROMACS best is:
> pdb2gmx with your PDB-file (including Dummies)
> then, you get the topology and the gro-file
> (including dummies).
> Then use editconf to generate the box, fill it with
> water by genbox and 
> add counter ions...then use grompp to generate your
> tpr-file.
> Even, if you have a topology file with dummies,
> GROMACS needs the 
> positions of the dummies and they are in the
> gro-file. If you don't have 
> any dummy-positions, just parameters for bonds,
> etc., GROMACS can't 
> guess them, I suppose.
> 
> 2)
> The quotes are just quotes...first, I think no one
> really cares about 
> them and second: I you don't like them, don't use
> Gromacs...;)
> 
> Regards
> 
> Maik Goette, Dipl. Biol.
> Max Planck Institute for Biophysical Chemistry
> Theoretical & computational biophysics department
> Am Fassberg 11
> 37077 Goettingen
> Germany
> Tel.  : ++49 551 201 2310
> Fax   : ++49 551 201 2302
> Email : mgoette[at]mpi-bpc.mpg.de
>          mgoette2[at]gwdg.de
> WWW   :
> http://www.mpibpc.gwdg.de/groups/grubmueller/
> 
> 
> Omololu wrote:
> > Hi,
> > 
> > i am new to gromacs. i must say thanks to the
> > developers of this program. it's simply great!
> > 
> > 1) my *.pdb file does not contain dummy atoms
> > (dummies) but my forcefield does. In my *.itp
> file, i
> > put the definition for all atoms including the
> > dummies. i used "editconf" to get a *.gro file but
> > this does not contain the dummies. How can i use
> the
> > program "grompp" without getting errors since
> there
> > are dummies in my *.itp file which are not in
> *.gro? 
> > i hope i do not have to edit the *.pdb file and
> put
> > the dummies in there.
> > 
> > 2) is there a way to turn of the silly quotes that
> the
> > programs write when they finish? Some of them seem
> to
> > be quite offensive. I tried getting rid of the
> > "gurgle.dat" file but then "ngmx" crashes when i
> try
> > to use it. Or is there a way to create my own
> > "gurgle.dat"?
> > 
> > thanks a lot for any help.
> > 
> > o.
> > 
> > ***************** SEEK GOD! *******************
> > 
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