For building membrane/protein systems I recommend charmm-gui.org
The server automatically builds the coordinates, which you should be
able to use
with any modeling program; CHARMM equilibration scripts are generated
as well
Krzysztof
On 9/2/10 6:20 AM, Justin A. Lemkul wrote:
Please keep all Gromacs-related correspondence on the gmx-users list.
I am not a private help service. I am CC'ing the message there;
please continue any discussion via the forum.
Creating a lipid bilayer is not a particularly easy task. You can
generate a leaflet by replicating the coordinates of one lipid
molecule in the x-y plane using genbox, then create the facing leaflet
by rotating the existing leaflet using editconf. Concatenate the
files and you have yourself a bilayer (which will need extensive
equilibration, of course). Adding water is trivial with genbox.
-Justin
praba vathy wrote:
Dear Sir,
I want to create a lipid bilayer in which protein is inserted and on
the top of insertion i need to put the water molecules and then at the
bottom as well. I don't understand that how to place the
molecules using Gromacs. Please give suggestions.
Regards,
Prabha. K
--
Krzysztof Kuczera
Professor
Departments of Chemistry and Molecular Biosciences
The University of Kansas
2010 Malott Hall
Lawrence, KS 66045
Tel: 785-864-5060 Fax: 785-864-5396 email: kkucz...@ku.edu
http://oolung.chem.ku.edu/~kuczera/home.html
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