[gmx-users] looking for gmx-tutorials

m b mic0404 at yahoo.com
Mon Dec 15 14:43:01 CET 2003

Raghunadha Reddy Burri  wrote:

> Dear gmx users,
> I am looking for gmx-tutorials to generates the tip5p water box with any 
> peptide. If you have idea please send for me.
> looking for positive reply.
> Bye
> RB 

you can use mkr0, a program you find in 
(this version on my homepage (which I cannot access
at the moment) is somewhat out-dated, if you want to have
a newer version that can also read/write pdb format let
me know and I'll forward it to you)

download mkr0.c and micutc.h to the same directory, 
and compile it with, e.g., gcc.
A short help text is included in the source file.
You need the coordinates of one single TIP5P (or any other
solvent molecule) centered approximately at the origin. 
You can use mkr0 to generate a box filled with that solvent
with any desired density and dimensions.
You can also exlude molecules that overlap with
(a) given solute(s) (Protein) if you provide a file with 
the solute coordinates (in xyz format)
The output is also a simple xyz format. To convert that
to pdb you can use, e.g., gOpenmol or babel.
Alternatively you can make only the water box and
then generate the solvated protein with genbox, a rather 
versatile prrogram that comes with Gromacs.


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