VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Oct 03 2007 - 08:23:07 CDT

Just to be clear, your equilibrated solvent cube does *not* need to be
large enough to envelop the molecule you want to solvate; part of the
point of the Solvate plugin is that it tiles the input solvent cube
through space as necessary to cover your solute. You just need a cube
that's large enough so that you can cover most solutes through a
reasonable number of copies of it. This is, in fact, what solvate does
when it is used with normal water as well, using an equilibrated TIP3
water box that is ~65 angstroms on a side.
Peter

lucie huynh wrote:
>
> Hi evryboby,
>
> I'd like to build a solvent box for a protein (30% methanol). I tried
> the options dedicated to nonstandard solvent but it seems that I did
> something wrong.
> I have a pdb and a psf file of methanol and its topology file. But my
> pdb file only define one molecule of methanol. Do I have to build a
> pdb file of the rigth number of methanol molecule needed for a solvent
> with 30% of methanol?
> I also did not understand the option "key selection" and box "padding".
> Do the nonstandard solvent option allow the generation of a solvent
> with different types of molecule?
> Or do I have to build one box of each (water and methanol) and then
> superimpose or combine them?
>
> Thanks a lot for any help or suggestion,
> Have a nice day!
>
> Lucie