[gmx-users] Coordinate file for charmm36 POPC

Ariel Leong ariel.leongsw at gmail.com
Thu Aug 14 13:20:47 CEST 2014

All the methods you mentioned can be used. If you do not need the water you
can simple delete the lines containing water atoms in Peter's coordinate

The value of xy in CHARMM-GUI refers to the size of membrane you need.

On Thu, Aug 14, 2014 at 6:46 PM, yashita thakur <yashta.thakur at gmail.com>

> Hello All
> I am trying to perform MD for protein ligand protein complex in popc lipid
> with
> charmm36 force field and also follow Justin A. Lemkul tutorial.
> As I am working for charmm force field I dont know from where I can get the
> lipid coordinate file for POPC as we cannot use  united-atom Berger model
> from Peter Tieleman as mention in tutorial.
> Can I use coordinate file Provided by Peter C. Lai:
> http://cesium.hyperfine.info/~peter/gromacs/popc36/
> But in this file it also include water so according to Justin tutorial its
> mention to use
> inflategro.pl and energy minimization and then only add water and ion. In
> this file when to use
> inflategro.pl??
> I also tried CHARMM-GUI but when I use only membrane then it generate only
> heterogeneous system and also ask for some ratio s1/s2 and also value of
> xy which I dont know.
> the following link also contain charmm36 coordinate file but  they provide
> in different time scale like popc-ns16.pdb. Which file should I choose.
> http://www.lobos.nih.gov/mbs/coords.shtml
> What to do??
> Some one please help..
> Warm Regards
> Yashita
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Best regards,
Leong Siew Wen
Institute for Research in Molecular Medicine
Universiti Sains Malaysia

“Making the simple complicated is commonplace; making the complicated
simple, awesomely simple, that’s creativity.”
 *- Charles Mingus-*

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