VMD-L Mailing List

From: Luis Rosales (ludwig_at_correo.biomedicas.unam.mx)
Date: Wed Apr 27 2005 - 04:12:08 CDT

Hi Huaer!

I think that the solvate plugin is limited to solvation in a water box,

However, the good news is that you can use VegaZZ
(http://users.unimi.it/ddl/vega/) to add a solvent cluster/box around your
molecule.

The bad news is that among the several included solvent types in VegaZZ, there
is no methanol/water mixture.

Anyway you can use vegaZZ to build your own solvent box, then you could use it
to solvate your molecule and voilá!!!
(I suppose that you should need to equilibrate your solvent mixture before
using it to build your solvent/DNA system...)

Hope this helps,

Ludovico

> -----Original Message-----
> From: owner-vmd-l_at_ks.uiuc.edu
> [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of Huaer XC
> Sent: Wednesday, April 27, 2005 1:28 AM
> To: vmd-l_at_ks.uiuc.edu
> Subject: vmd-l: Solvate plugin
>
> Hi, all:
>
> Can I use VMD's solvate plugin to build a box of mixture of 80%
> ethanol and 20% water to contain a DNA helex? how can I generate the
> input files? Can somebody points me to some webpages or just give me a
> hint. Thanks in advance...:)
> Best,
> Huaer
>