Re: Problem with using autoPSF on TMCL lipid

From: Giacomo Fiorin (
Date: Fri Dec 16 2016 - 11:18:21 CST

Hello Saleh, TMCL is cardiolipin in the CHARMM naming scheme.

Keep in mind that only a handful of cardiolipin (1-2% molar fraction,
please check the literature) is present in the E Coli membrane.

The CHARMM-GUI server is an instrument that simplifies input creation, but
can never replace the best judgment of the investigator who is using it
(i.e., you). Specifically, it does not know what kind of simulation you
will perform.

If you decide to use a 100 Å x 100 Å bilayer, there will be maybe 3 or 5
cardiolipin molecules in the entire membrane. I leave it up to you to
decide whether their addition will positively affect your simulation. For
sure you will be forced to run longer than a few hundreds of ns, because
cardiolipin is a four-tail, 72-carbon behemoth that moves much more slowly
than the more common two-tail phospholipids.

There are of course published MD simulations of cardiolipin-containing
bilayers, but it's very rare to find any that were meaningful in terms of
bilayer size and simulation length.


On Fri, Dec 16, 2016 at 11:40 AM, Jeff Comer <> wrote:

> Dear Saleh,
> Why would you use autoPSF (the VMD plug-in?) together with CHARMM-GUI.
> CHARMM-GUI already generates the psf for you and generally does a
> better job at it than autoPSF. I see no reason to use autoPSF.
> Regards,
> Jeff
> –––––––––––––––––––––––––––––––––––———————
> Jeffrey Comer, PhD
> Assistant Professor
> Institute of Computational Comparative Medicine
> Nanotechnology Innovation Center of Kansas State
> Kansas State University
> Office: P-213 Mosier Hall
> Phone: 785-532-6311
> Website:
> On Fri, Dec 16, 2016 at 10:11 AM, salehesam101 . <>
> wrote:
> > Greetings,
> >
> > I am attempting to develop a bilayer with the composition of that f
> E.coli.
> > It seems that anytime I attempt to run autoPSF, i run into a problem with
> > the composition of one of the lipids I am using, namely TMCL (from
> Charm-Gui
> > membrane generator). It seems that none of the topology files I uploaded
> > from the toppar folder I was given from Charm-Gui is recognized by
> autoPSF
> > for this particular lipid. All other lipids were recognized, but not
> >
> > Is this an issue with autoPSF or the topology file?
> >
> > How can I solve this?
> >
> >
> > Best,
> > Saleh Al-Khalifa
> >
> >

Giacomo Fiorin
Associate Professor of Research
Institute for Computational Molecular Science (ICMS)
College of Science and Technology, Temple University
1925 North 12th Street (035-07), Room 704D
Philadelphia, PA 19122-1801
Phone: +1-215-204-4213
Lab page:
*"As computer programmers we have a responsibility to make sure that we run
the computers instead of the computers running us."*  - Steve Oualline

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