[gmx-users] dummies

[Maik Goette]

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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