[gmx-users] Regarding membrane construction

[Venkat Reddy]

Dear Justin,
I have tried the command
genbox -cp protein.gro -cs membrane.gro -o protein_in_membrane.gro
 but it got hanged. Is there something wrong with the command?


On Mon, Jun 9, 2014 at 5:50 PM, 陈功 <gchen511 at gmail.com> wrote:

> Thanks for correction. i appriciate it :)
> Chen Gong
>
>
>
>
>
> From: Justin Lemkul
> Date: 2014-06-09 19:58
> To: gmx-users
> Subject: Re: [gmx-users] Regarding membrane construction
>
>
> On 6/9/14, 3:22 AM, 陈功 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
>
> Packmol is a good choice, but the approach above with genbox likely won't
> work.
>   It will produce a random insertion of lipids.  The simplest way within
> Gromacs
> to create a membrane of sufficient size is to place the protein in a
> suitably
> sized box (with editconf) and then
>
> genbox -cp protein.gro -cs membrane.gro -o protein_in_membrane.gro
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036