[gmx-users] Coordinate file for charmm36 POPC

yashita thakur yashta.thakur at gmail.com
Thu Aug 14 12:47:05 CEST 2014

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:

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

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.


What to do??

Some one please help..

Warm Regards

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