[gmx-users] dummies

Omololu prayerz at yahoo.com
Wed Aug 31 20:20:33 CEST 2005


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

thanks a lot for any help.


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