[gmx-users] Regarding membrane construction
venkat4bt at gmail.com
Mon Jun 9 14:13:16 CEST 2014
Thank you Justin.
On Mon, Jun 9, 2014 at 5:28 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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
>> -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
>> 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 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
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With Best Wishes
Venkat Reddy Chirasani
Laboratory of Computational Biophysics
Department of Biotechnology
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