From: Axel Kohlmeyer (
Date: Thu Dec 30 2010 - 14:43:20 CST

On Wed, Dec 29, 2010 at 10:55 AM, Bharat Kumar <> wrote:
> Hi
> I minimized a protein embedded in a 100 X 100 POPC lipid layer with MOE. I
> want to also minimize the output pdb of MOE using NAMD. But the MOE
> minimized PDB has some broken lipids. When I generate PSF using psfgen i
> find some weird bond formations. And also the autopsf-generated PSF and PDB
> files are half less dense than the input PDB. Half lipids go missing. So I
> am trying to remove all the lipid fragments that are flying apart. I am
> doing this manually.

hi bharat,

what you are describing doesn't make any sense.
a psf file has no coordinate information. only atom type,
mass, charge, and bonding topology (bonds, angles and so on).

furthermore, the mathematical formulation of the charmm force field
makes it impossible to break bonds. it looks like you are confused
about periodic boundary conditions and coordinate wrapping (or not).

> Does VMD contain any tool to fix these sort of files? I think I can fix the
> weird bonds by removing the fragments. But I cannot understand the reduction
> in density of lipid layer. Can you please explain why there is a reduction
> in lipids after psf?

as above, there should be no reduction in the number of particles or
density unless you do something wrong. it is also not entirely clear
to me, why you need to generate a psf file _after_ your calculation?
what is wrong with the one you created for the calculation?


> Thanks,
> Bharat.

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.