From: Bharat Kumar (
Date: Thu Dec 30 2010 - 18:31:21 CST

Hi Axel,

I think I lacked clarity in my first email.

To restate, I want to minimize a PDB file, which has some broken
lipids.(This particular PDB was generated by MOE on minimization of a PDB
transmembrane protein embedded in a POPC ). Now I tried to generate psf, pdb
using autopsf. The output pdb (file_autopsf.pdb) is less dense, with
approximately half the lipid molecules missing.

And there were formations of some weird bonds at the broken lipid sites. So
I tried to manually remove the broken lipid fragments from the PDB. Then
again I generated psf, pdb using autopsf. This time some of the broken bonds
were absent. But there was no improvement in the lipid molecules.(They were
still half the original number) Can you please suggest how to handle these
broken lipid files? And why is the lipid number reduced? is this because of
bad input file?

I am trying to get acquainted with VMD and NAMD. So I am also trying to
perform simulation using NAMD.

Thanks for your reply.


On Thu, Dec 30, 2010 at 3:43 PM, Axel Kohlmeyer <> wrote:

> 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
> > 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?
> axel.
> >
> > Thanks,
> > Bharat.
> >
> --
> Dr. Axel Kohlmeyer
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.