Re: Problem with using autoPSF on TMCL lipid

From: Jeff Comer (
Date: Fri Dec 16 2016 - 10:40:17 CST

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.


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

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 TMCL.
> Is this an issue with autoPSF or the topology file?
> How can I solve this?
> Best,
> Saleh Al-Khalifa

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