VMD-L Mailing List

From: Ioana Cozmuta (ioana_at_nas.nasa.gov)
Date: Tue Jan 14 2003 - 20:05:46 CST

Dear VMD-users,

I have a cylindrical pore and I want to add water only inside the pore.
I did create in vmd a psf file corresponding to my initial pdb structure
and also used the minmax procedure to calculate the extremes of the pore.
then I just used the solvate extension in vmd
solvate <psffile> <pdbfile> -o new -minmax { {minvalues} {maxvalues}}

Indeed there were water molecules added but the whole pore is now inserted
into a big box. Is there an additional option that I can use to tell VMD
to add waters only inside the xmin, ymin, zmin, xmax, ymax, zmax of the
pore and not to add any outside it?

Thank you in advance,
Ioana

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* Ioana Cozmuta, PhD * *
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