VMD-L Mailing List

From: Leandro Martínez (leandromartinez98_at_gmail.com)
Date: Wed Oct 03 2007 - 08:35:19 CDT

Hi Lucie,
You can try the packmol package, it was written for that:
http://www.ime.unicamp.br/~martinez/packmol
Best regards,
Leandro.

On 10/3/07, lucie huynh <luciehuynh_at_gmail.com> 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
>