VMD-L Mailing List

From: Pawel Kedzierski (pawel.kedzierski_at_pwr.edu.pl)
Date: Fri Nov 25 2016 - 01:27:57 CST

W dniu 24.11.2016 o 17:30, Dawid das pisze:
> Dear VMD Experts,
>
> I have a structure in XYZ file format and I would like to solavate it
> with Solvate plugin.
> However, when I choose minimum and maximum dimensions of the box, I
> get my box of
> water molecules but water molecules that are too close to my structure
> are not deleted. Is
> there a simple way to do proper solvation of structure in a XYZ file?
Dear Dawid,
Please check first if you have the checkbox labeled "Waterbox only"
unselected. If this was on, you got a box of pure water as a new
molecule without your solute (but of course it overlaps with the solute
in the OpenGL window so it may be confusing by simply viewing it).

If this guess is wrong then I can't tell why your structure is not
solvated properly, but still you should be able to work around the
problem using selections:

(not water) or (not (within 2.4 of (not water)))

This should select the solute (as "not water") and all water further
away than 2.4A from the solute (the default distance used in the Solvate
plugin).
Then by File -> Save coordinates you can save this selection to a new
xyz file.
Greetings,
Pawel
>
> Best regards,
> Dawid Grabarek