[gmx-users] Tutorial KALP-15 in DPPC

Shima Arasteh shima_arasteh2001 at yahoo.com
Fri Jun 15 16:34:04 CEST 2012

 Thanks for your reply.
But one more question: what about when the applied lipid bilayer is POPC? Is this .top file (topol_dppc) useful yet? How come?
You know, my main problem is that I don't know where this .top file come from?


 From: Justin A. Lemkul <jalemkul at vt.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Friday, June 15, 2012 6:57 PM
Subject: Re: [gmx-users] Tutorial KALP-15 in DPPC

On 6/15/12 10:25 AM, Shima Arasteh wrote:
>   Dear gmx users,
> I am doing KALP15 in DPPC following the Justin tutorial
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html
> . In the second step, the first command is grompp as follow:
> grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr
> I want to know if the topol_dppc.top in this command is the .top file which produced by pdb2gmx at the beginning of the first step? If not, so what is that?

No, it is a different topology provided to you by the tutorial.  Please note the 
statements in the tutorial to this effect; it is the only time it is used.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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