[gmx-users] make_ndx/genbox

David spoel at xray.bmc.uu.se
Wed Dec 18 07:41:12 CET 2002

On Tue, 2002-12-17 at 23:16, Senthil Kandasamy wrote:

> >/>/ I  need to insert a large molecule into a system in a region with mostly
> >/>/ waters. I need to remove ALL the conflicting water molecules before
> >/>/ insertion.
> >/>/  
> >/Why don't you use genbox?
> Because, I am not just trying to solvate a protein.
> I am trying to insert a protein in the neighbourhood of a lipid bilayer and 
> other peptides. I assumed genbox could not do it.  or can it...??? 
Yes it can. Just make sure your protein is located in the right position
in the box and that the box sizes are equal for solvent and protein. The
genbox will cut out whatever needs to be cut out, and put the protein

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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