VMD-L Mailing List

From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Sat Apr 27 2013 - 20:34:13 CDT

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