VMD-L Mailing List
From: Pawel Kedzierski (pawel.kedzierski_at_pwr.edu.pl)
Date: Fri Nov 25 2016 - 03:20:37 CST
W dniu 25.11.2016 o 09:14, Dawid das pisze:
> 2016-11-25 8:27 GMT+01:00 Pawel Kedzierski
> <pawel.kedzierski_at_pwr.edu.pl <mailto:pawel.kedzierski_at_pwr.edu.pl>>:
> 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).
> It was selected. Otherwise VMD says ``error solvate: need file
> names'' as I do not have PDB and PSF files.
> 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.
> I thought it should have worked, but unfortunately, the added water
> box is a new molecule (with new Molecule ID) so I do not know how to
> select visualizationfor molecules with different IDs. Is that possible
> at all?
A separate molecule is a separate molecule, period.
You could save the water box to another file and combine the two in an
editor, then load them as a single entity back in vmd and make use of my
Or, you can generate PDB and PSF files using e.g. Molefacture plugin:
1. Load your molecule from XYZ
2. Extensions -> Modeling -> Molefacture
3. Type "all" as the requested selection
4. In the Molefacture window, File -> Write pdb and psf files
Then you can use these PSF+PDB with Solvate.
Yet another (scriptable) way is to use selections from VMD command line:
mol new molecule.xyz
set sel [atomselect top "all"]
$sel writepsf molecule.psf
$sel writepdb molecule.pdb
Note that you can also use solvate from VMD command line:
solvate molecule.psf molecule.pdb -o solvated -t 5
In all cases you get the result as pair of PSF+PDB files, not XYZ, and
you may loose some precision as PDB format is limited to third decimal
- text/x-vcard attachment: pawel_kedzierski.vcf