[gmx-users] insert protein in membrane

Jochen Hub jhub at gwdg.de
Tue Dec 18 14:00:54 CET 2007

Magnus Andersson wrote:
> Hi all,
> I have a .top file of a membrane protein (from an earlier project).
> I also managed to generate a .gro file of a simple "membrane" consisting
> of Argon atoms, of a certain volume.
Did I get you right that you do not have a structure (.pdb, .gro) of the 
protein? As soon as this is solved, use

genbox -cp prot.gro -cs lipid.gro

And make sure that the CRYST lines somehow match, otherwise genbox fills 
up the protein box with the membrane.

> How can I insert the protein into this membrane? I guess it somehow
> involves how to combine the protein .top file and the membrane .gro file I
> already have.
> (I have tried generating a .top file from the membrane .gro file
> (pdb2gmx), doesn't work. It deletes "duplicate atoms".
> Can someone give me step-by-step instructions to this problem.
> Greatly appreciate your help!
> /Magnus

Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de

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