[gmx-users] looking for gmx-tutorials

Raghunadha Reddy Burri burri at heineken.chemie.uni-dortmund.de
Mon Dec 15 15:47:00 CET 2003

Dear Michael,
Thanks for your reply, I am happy to see your mail, your program looks very 
sound, those are very useful for me, please send for me new version of that.
Thank you very much



On Monday 15 December 2003 14:42, m b wrote:
> 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
> http://www.ucl.ac.uk/~uccambr/software.html
> (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.
> regards,
> Michael

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