[gmx-users] make hole

[Itamar Kass]

Dear Nada,

In order to run the script please use

perl ../perl_files/make_hole.pl -f dmpc_npat.pdb -o outbilayer.pdb -r  
1 -lipat P -lipid DMP

–f is the input file
–o is the output file
–r is the radius of the hole
–lipat is the molecule which determines if the dmpc molecule should  
be removed

Good luck, Itamar.

On Jan 11, 2006, at 4:23 PM, nada taib wrote:

>  dear professor
>
> I would try to perform MD of protein inserted in a popc
>  lipid bilayer but i' don't know how to make hole in popc
> and how to work with make-hole.pl
>  I will really appreciate if you can help me
>
> think you
> Nada TAIB
> Institut Européen de Chimie et de Biologie (IECB)
> CNRS UMR 5144 Molécules, Biomolécules et Objets Supramoléculaires  
> (MoBIOS)
> 2, rue Robert Escarpit - 33607 Pessac Cedex - France
> Tél. : 33 (0)5 40 00 30 31
> Fax. : 33 (0)5 40 00 30 73
> http://www.iecb.u-bordeaux.fr
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===========================================
| Itamar Kass
| The Alexander Silberman
| Institute of Life Sciences
| Department of Biological Chemistry
| The Hebrew University, Givat-Ram
| Jerusalem, 91904, Israel
| Tel: +972-(0)2-6585194
| Fax: +972-(0)2-6584329
| Email: ikass at cc.huji.ac.il
| Homepage: http://www.ls.huji.ac.il/~membranelab/itamar/ 
itamar_homepage.html
============================================


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