[gmx-users] Tutorial KALP-15 in DPPC

[Justin A. Lemkul]

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

========================================