VMD-L Mailing List

From: lucie huynh (luciehuynh_at_gmail.com)
Date: Wed Oct 03 2007 - 07:53:21 CDT

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