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.
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