VMD-L Mailing List

From: Steven Neumann (s.neumann08_at_gmail.com)
Date: Mon Oct 01 2012 - 02:58:44 CDT

Dear users,

I am trying to solvate my assymetric protein in water box:

package require solvate
solvate A_new.psf A_new.pdb -b 2 -minmax {{-10 -10 -10} {10 10 10}} -o Solv

When I open pdb file Solv.pdb I see my protein solvated in the
specified water box dimensions. however, when I type:

pbc box

The box boundaries are in a completely different place that my
solvated system. How can I reset cooridante of my initial structure so
that it will appear inside the pbc box?

Thank you,

Steve