VMD-L Mailing List
From: surya narayanan chandrasekaran (sonofsunsurya_at_gmail.com)
Date: Wed Nov 28 2018 - 03:27:16 CST
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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 tip4p.top -ws 23 -o ice-prot
-ks "name OH2"
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solvate prot1.psf prot1.pdb -rotate -spsf ICES-hex.psf -spdb ICES-hex.pdb
-stop tip4p.top -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
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Warm regards,
Dr. Suryanarayanan C
- Next message: Peter Freddolino: "Re: REG building non standard solvent simulation box."
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