From: Francesco Pietra (
Date: Mon Dec 07 2009 - 01:31:46 CST

As to paratool it was not laziness. I don't have Gaussian so that I
have to wait until Paratool runs (as promised by Jan) on Gamess US.

---------- Forwarded message ----------
From: Francesco Pietra <>
Date: Sun, Dec 6, 2009 at 8:24 PM
Subject: Re: vmd-l: CG lipid bilayer vmd 1.8.7
To: Anton Arkhipov <>
Cc: vmd <>

Hi Anton:
Thanks for completing the panorama. As you provided bead definitions
for both DOPC (dopc.cgc) and POPC (lipid.cgc), do you have also
dopc.psf? I extracted the single dopc molecule pdb from Feller's
equilibrated dopc bilayer but AutoPSF requests parameters, indicating
that the missing ones can be obtained with Paratool (which I have
never used yet). In my hands, the CG Builder does not work without
both psf and pdb,

For POPC (which for final work I would prefer to DOPC) I have both pdb
and psf but no equilibrated bilayer found on the web. I could build
the cg POPC bilayer from my non equilibrated bilayer (I just made a
80x80 membrane with Balabin plugin). Probably, however, equilibration
should be first carried out all-atoms.


On Sun, Dec 6, 2009 at 7:35 AM, Anton Arkhipov <> wrote:
> Hi Francesco,
> Just to add to whatever help you got already:
> for an rbcg bilayer, take an equilibrated all-atom bilayer, and convert it
> to rbcg. If you want to be extra careful, then you can solvate the result
> with rbcg water and use rbcg simulation to equilibrate the bilayer further.
> For sbcg, there's no direct conversion available, but it's not necessary,
> because the model is extremely simple - just two beads connected by a spring
> make one "molecule", and a bunch of such molecules constitute a leaflet. So
> if you need an sbcg bilayer, it's very simple to just create a pdb with such
> molecules by hand. You cna put those sbcg "molecules" uniformly distributed
> in the bilayer, and then equilibrate them with sbcg simulations.
> Anton.
> On Dec 2, 2009, at 10:13 AM, Francesco Pietra wrote:
>> Hi;
>> After I posted the subject problem as secondary matter, I carried out
>> an accurate search on the web, unable to find an equilibrated rbcg
>> lipid bilayer for vmd 1.8.7/namd martini implementation (or a plain
>> procedure to get it from scratch). As for sbcg, I guess that direct
>> conversion from an equilibrated all-atoms lipid bilayer will not work.
>> Thanks for info.
>> francesco pietra