VMD-L Mailing List

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Tue Nov 06 2012 - 13:39:07 CST

Hi,

Create the boxes, equilibrate them for a bit, then insert your protein and
remove the overlapping solvent molecules. The membrane protein
tutorial<http://www.ks.uiuc.edu/Training/Tutorials/science/membrane/mem-tutorial.pdf>shows
how to remove the lipids that overlap the protein. I'm sure it would
be easy to adapt for solvent molecules. Perhaps somebody has an easier way,
this is just off the top of my head:)

Best regards,
Ajasja

On 6 November 2012 18:01, <amin_at_imtech.res.in> wrote:

> Dear all,
> I want to solvate my protein with water and sucrose at a defined
> concentration
> eg 30% sucrose solution. Can someone please guide me how to do this? While
> trying few things, I have made some boxes having different number of water
> and
> sucrose molecules with packmol but have little idea on how to proceed. Any
> suggestions would be appreciated.
> Regards.
> Amin.
>
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