From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Sat Dec 04 2010 - 14:57:11 CST

You can also try Charmm-gui
<http://www.charmm-gui.org/?doc=input/membrane>. Unfortunately it
only produces charmm input files for equilibration, but an
unequilibrated pdb/psf pair is easy to obtain. I had best result with
running the equilibration in charmm and later switching to NAMD, but the
whole equilibration process could be done in NAMD alone.

regards,
Ajasja

On Thu, Dec 2, 2010 at 17:39, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> hi pat,
>
> On Thu, Dec 2, 2010 at 8:15 AM, Patrick Fleming <patrickflemin_at_gmail.com>
> wrote:
> > I would like to equilibrate a phospholipid membrane other than the two
> > supplied with VMD. I have a PDB file of the new lipid but it appears that
> I
> > would have to make separate PDB files for each lipid molecule in order to
> > use psfgen. It this really necessary?
> >
> > In other words, given a PDB file of many dilaurylPC molecules and the
> > appropriate topology and parameter files how do I generate the psf file?
>
> i would just create the psf for a single lipid molecule from a single
> molecule
> pdb file and then replicate the lipid and write out the psf for that. since
> the
> psf file has no coordinates, it doesn't matter whether the replicated
> system
> is reasonable for as long as the bonding topology is correct.
>
> one way to get the replicated psf would be to use the topotools plugin.
>
> package require topotools
> mol new my.psf waitfor all
> mol addfile my pdb waitfor all
>
> ::TopoTools::replicatemol top 1 1 <# of lipids>
>
> animate write psf replicated.psf
>
> cheers,
> axel.
>
>
>
> >
> > Pat Fleming
> >
> > --
> > _o
> > ' / '- __o
> > _|\ \<,
> > ....|......( )/( )...
> >
> >
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>
>