VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Wed Nov 28 2018 - 07:51:17 CST

Does your solvent pdb have segid QQQ for all solvent atoms? That is the
most common point of failure for nonstandard solvents (see the notes in the
solvate documentation at
https://www.ks.uiuc.edu/Research/vmd/plugins/solvate/)
Best,
Peter

On Wed, Nov 28, 2018 at 5:51 AM surya narayanan chandrasekaran <
sonofsunsurya_at_gmail.com> wrote:

> 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"
> ----------------------------------------------------------------------
> 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
>
> ---------------------------------------------------------------
>
>
> Warm regards,
> Dr. Suryanarayanan C
>
>
>