[gmx-users] Regarding membrane construction
gchen511 at gmail.com
Mon Jun 9 09:22:55 CEST 2014
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.
From: Venkat Reddy
Date: 2014-06-09 15:31
To: Discussion list for GROMACS users
Subject: [gmx-users] Regarding membrane construction
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.
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