[gmx-users] Coordinate file for charmm36 POPC

[yashita thakur]

Thank you Ariel for your reply.

How to know what should be the size of system.
Like it should be 30,000 or more. Then how to mention it.
secondly how to know how many lipid POPC should be added. In united-atom
Berger model from Peter Tieleman POPC number is 128.
Should I ass that much or more that that??

Can I use Peter's coordinate file deleting water and follow the same step
as mention in Justin A. Lemkul tutorial??

Thank you.



Warm Regards
Yashita Thakur
976-614-4219


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On Thu, Aug 14, 2014 at 4:50 PM, Ariel Leong <ariel.leongsw at gmail.com>
wrote:

> 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
> file.
>
> 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>
> wrote:
>
> > 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
>
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