[gmx-users] All-atom topologies for lipid head groups

[Ioannis Beis]

Dear Gromacs users,

I am a new user and I am trying to study the physical properties of  
the interactions between cytosolic proteins and lipids. I have created  
the Berger-Gromos combination, as described by Mr. Justin Lemkul in  
his KALP15 in DPPC tutorial, as well as Berger-OplsAA, as described by  
Mr. Chris Neale in gromacs mailing list. All-atom topologies might  
turn out to be crucial in my work, both in the results and the data  
analysis (e.g. H-bonds).

Even if the all-atom model of Opls-AA is used for the proteins, the  
lipid head groups would still have a united-atom description and  
therefore the interactions can't be treated in an all-atom level.

I thought of creating a new topology for the lipid head groups under a  
head.itp file, by using parameter values from Dundee server and/or  
Opls-AA, even though I do not know yet exactly how and I feel very  
unsure about the eventual incorporation into the Berger-OplsAA  
combination. Then taking single lipids of pre-equilibrated membranes,  
editing accordingly the coordinate file (i.e. replacement of polar  
head atoms and use of new coordinates, names and residue names for  
them) and subsequently building bilayers.

I would really appreciate if someone could send suggestions. In  
addition, if someone already has an all-atom description of lipid  
head-groups compatible with a protein-membrane force field combination  
with all-atom protein description, I would be grateful if he/she could  
share.

Thank you in advance.