From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Wed Mar 30 2016 - 08:08:14 CDT
I usually put 5-10 Angstrem spacing on each side.
And then I get the cell basis vector using min/max (sometimes adding a 0.5
A just to be on the safe side).
### center the protein and also measure the min/max
set allp [atomselect top "all"]
measure center $allp
measure minmax $allp
set dims [measure minmax $allp]; vecsub [lindex $dims 1] [lindex $dims 0]
# center the protein
$allp moveby [vecinvert [measure center $allp]]
On 30 March 2016 at 14:51, faride badalkhani <farideh.khamseh_at_gmail.com>
> Dear all,
> Could you give me some information how to determine the size of water box
> package require solvate
> solvate system.psf system.pdb -t X -o system_wb
> And, what is the best way to determine cellbasisvectores? Is that
> reasonable to use minmax command and then use the maximum coordinate?
> Truly yours,
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