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?
Sincerely,
Shima
________________________________
From: Justin A. Lemkul <jalem...@vt.edu>
To: Shima Arasteh <shima_arasteh2...@yahoo.com>; Discussion list for GROMACS
users <gmx-users@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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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