Re: construct a protein surrounded by membrane

From: mashaojie (
Date: Fri Mar 19 2004 - 08:41:20 CST

    I have got a channel protein structure and construct psffile and pdbfile from original pdbfile,
I want to get the structure that the protien surrounded by cell membrane, I want to get psffile and pdbfile.
  The problems is how to embed this protein into membrane, if I dig a big hole, I can not make protein close enough to membrane. If I dig a small one, there are so many overlapped atoms in I don't know how to solve it. The membrane can be obtain by the plugins of vmd.
----- Original Message -----
From: "Josef Scheiber" <>
To: "mashaojie" <>
Sent: Friday, March 19, 2004 6:53 PM
Subject: Re: namd-l: construct a protein surrounded by membrane


what is your concrete task? Do you want to bring such a complex into NAMD or do
you want to generate a structure file (e.g. mol2 or pdb) representing this

Bye, Sepp

Zitat von mashaojie <>:

> Hi:
> I want to construct a protein surrounded by cell membrane ,I don't know how
> to do it .
> please help me.

Josef Scheiber <>

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