From: Jadzia Dax (
Date: Tue Jan 02 2018 - 01:29:30 CST

Hi Everyone, and a happy new.

On this
NAMD/VMD page here is written:

*As with dihedrals, the order of atoms within an ​​improper may be
> reversed. As shown below, impropers are specified by the IMPR statement
> followed by sets of four atoms, with the central atom to which the other
> three are bonded typically listed first.​*

Why can the direction be reversed with impropers? As far as I can see this
would change the central atom. The three orbital atoms should be
exchangable of course, but this would rather be any permutation of the last
three atoms.

The reason why I am concerned with this topic is that I have rtf/prm files
for a ligand prepared with CGenFF. The rtf file has one Improper. And when
I create the psf file with VMD/psfgen then the psf file has the atoms in
reversed order than in the rtf-file. But the prm-file still has the
original order. Thus my simulations (not with NAMD but with CP2K) fail
immediately because the it cannot find the parameters for this improper.

Any help or comment is appreciated.

Best wishes,