VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Nov 06 2012 - 13:47:56 CST

On Tue, Nov 6, 2012 at 6:01 PM, <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
>

kindly look through tutorials and publications
that do similar things. a mailing list is no
replacement for learning the tools of the trade.

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
>

well, you need to equilibrate your mixture boxes.
do you have proper force field data/parameters yet?
sugars can be tricky...

once you have large enough and well euqilibrated
mixture boxes, you can use the same tools to do
the solvation that are used with pure water. i.e.
replicate the box until the resulting box is large
enough to contain the entire protein plus ample
safety space. due to the size of the sugars, you
need more safety so that you don't have periodic
images coupled through a single molecule.

then you equilibrate the resulting system as if it
was a protein/water or protein/electrolyte system.

there are plenty tutorials for that.

cheers,
     axel.

suggestions would be appreciated.
> Regards.
> Amin.
>
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-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.