[gmx-users] Regarding membrane construction

[Venkat Reddy]

Thank you Chen for the quick reply. I will try both options.


On Mon, Jun 9, 2014 at 12:52 PM, 陈功 <gchen511 at gmail.com> wrote:

> Dear Venkat,
> I guess there are some other methods to generate  new lipid bilayer
> construct by using genbox -cp your_membrane_protein -ci lipid_monomer -nmol
> xxxcalculate by yourself -try 1000 -cs solovents.gro -p top.top -o
> new_conf.gro or using editconf & cat ...Another way, you can try the script
> packmol. Be more patient.  haha, I m also a new gmx user.
> Good  luck,
> chen gong
>
>
>
>
>
>
> From: Venkat Reddy
> Date: 2014-06-09 15:31
> To: Discussion list for GROMACS users
> Subject: [gmx-users] Regarding membrane construction
> Dear all,
> I am studying a membrane protein of length 288 residues. I want to simulate
> in a DPPC bilayer. I have downloaded dppc equilibrated bilayer from Peter
> Tieleman's website as directed by Justin in his membrane-protein tutorial.
> But I found 128 lipid membrane is not enough for my protein. From the
> literature, I found I need  81 lipids in each leaflet. How can I construct
> a 162 lipid equilibrated bilayer? I tried CHARMM-GUI to build it. But the
> equilibration is giving RATTLE error. Please help me in this regard.
>
> Thank you
>
> Venkat
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-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036