[gmx-users] hydroxy oxygen in lipid

medeawan at sohu.com medeawan at sohu.com
Fri Mar 12 05:26:02 CET 2004

dear all,
I have download the lipid.itp and dppc.itp from http://www.gromacs.org/topologies/force_fields.php, 
and download the topology of dppc from http://moose.bio.ucalgary.ca/Downloads/, in order to 
simulate a system of peptide and membrane.

But my membrame is a mixture of dppc and cardiolipin, which contain a hydroxy that most lipids 
haven't. There is not the atom type "LOA" in the lipid.itp, and I can't find any lipid topology 
file that contain OA. 

One suggestion is to use PRODRG, but the charge it provided looks so different from the other 
lipids' topology in http://moose.bio.ucalgary.ca/Downloads/.

Someone suggest me to write a topology of cardiolipin by myself, OA use the parameters in
ffgmx force field, other atoms use lipid force field (imitate the dppc topology file). But there 
are still many problems, like parameters of the bond, angle, dihedral... that contain both OA and Lxx.

Another question is how to get the "normal" conformation (straight and parallel carbo legs)of lipids?
Like the ones in http://moose.bio.ucalgary.ca/Downloads/ , these kind of conformations are suitable 
to use as initial structures to create lipid bilyers.

Anyone has some idea about these?
Thanks in advance.

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