Ioannis Beis wrote:
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.
It sounds to me like you're trying to create a Frankenstein force field. Why
wouldn't a UA representation of the lipids work? For hydrogen bonding, all
polar groups are represented with explicit H atoms. This is generally true of
all UA force fields, for lipids and proteins alike.
If you really want an AA representation of your molecules, you're probably
better off just applying the CHARMM force field to the whole system. The latest
version of Gromacs supports CHARMM, which includes a number of common lipids.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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