From: surya narayanan chandrasekaran (
Date: Wed Nov 28 2018 - 03:27:16 CST

Dear all,
             I was trying to build ice box around my protein using solvate
plugin and gui and always end up in one replica of my equilibriated box. So
here are the details i have ice box of TIP4P around 20 Angst and i am
trying to build around my protein always end up in single box its not
completly built around the protein.

Here are the commands i have tried.
solvate prot1.psf prot1.pdb -s W -minmax {{-45 -45 -45} {45 45 45}} -rotate
-spsf ICES-hex.psf -spdb ICES-hex.pdb -stop -ws 23 -o ice-prot
-ks "name OH2"
solvate prot1.psf prot1.pdb -rotate -spsf ICES-hex.psf -spdb ICES-hex.pdb
-stop -t 100 -o ice-prot -ks "name OH2"

and ice box is hexagon shape as ICE structure of water.
psfgen) reading structure from psf file ice.psf
psfgen) Unable to add (duplicate?) residue U:2


Warm regards,
Dr. Suryanarayanan C