From: Wenhao Liu (
Date: Sat Apr 27 2013 - 21:14:03 CDT

Thank you Chris! I will try topotools!

On Sat, Apr 27, 2013 at 9:34 PM, Mayne, Christopher G

> As far as I am aware, Molefacture doesn't have a mechanism to define
> impropers when writing to a PSF file. You can, however, load the PSF/PDB
> generated by Molefacture back into VMD, use TopoTools to add any necessary
> impropers, and rewrite the PSF file.
> Christopher Mayne
> On Apr 27, 2013, at 3:39 PM, Wenhao Liu wrote:
> > Hi VMD developers,
> > In the Molefacture plugin, I built one molecule, and I saved psf, pdb
> and top. They looks fine except there is no improper list in the psf and
> top files, I've used the force planar when I build the structure, so I am
> quite confused about how to get the improper lists? Or maybe the improper
> list in the psf file is not necessary as long as I have improper parameters
> in the parameter files, NAMD will assign the paramters for these 4 atoms?
> Thanks!
> >
> > Wenhao