Justin A. Lemkul wrote:
Krzysztof Mlynarczyk wrote:
Hello,
On Peter Tieleman's website we can find topologies for various popular
lipids. However those seem to be valid for the deprecated GROMOS87
force field. The g96_lipids.itp file is still unavailable. I'd like to
run a simulation of 7TM protein embedded into POPC membrane. G43a2x
seems to be a reasonable choice for this purpose. I still need the
parameters for my lipids. I am aware that combining parameters from
different force fields might lead to a disaster, that's why I want to
ask you:
1. Do you know any papers where POPC membrane and G43a2 force field
was used?
I've not seen one, because it has been known for some time that early
Gromos96 parameter sets did not reproduce long alkyl chain properties
particularly well.
Quick amendment - modifications to 43a2 and 45a3 have been made to better
reproduce lipid properties. Both are available for download on the Gromacs site
and you can probably track down the references, as well.
Sorry, read that one wrong the first time :)
-Justin
2. If not, is there any way to derive the proper parameters for the
force field of my choice using the lipid parameters from Peter
Tieleman's website or e.g. the parameters published by Andreas Kukol
for G53a6?
I don't see why you need to do such reverse engineering. The Kukol
parameters for lipids under 53a6 can be directly combined with a G53a6
protein without any issues; I believe that was the purpose of the whole
new derivation :)
As an aside, you are quite right that multiple force fields within the
same simulation is incorrect. However, the Berger lipid parameters may
be an exception to this rule, since they are really a hybridized version
of OPLS-UA and Gromos87 parameters (some of which were modified anyway),
so they really don't belong to any one particular force field. The
Berger/G87 combination is widely used, but essentially amounts to the
following: lipid interactions are Berger-Berger or OPLS-OPLS
interactions, while protein-lipid interations are Berger-G87, and
protein-protein interactions are G87-G87. You can see quite quickly why
things become complicated!
Based on a discussion I had with Dr. Tieleman, it seems to be reasonable
to use the G96 parameter set of your choice in conjunction with
lipid.itp (Berger lipids), although other approaches may be more
rigorously correct (pure G96 parameters such as those by Kukol, pure
OPLS recently derived by Ulmschneider, or the modifications to the
Berger parameters from the Tieleman group, to name a few). If you want
to use a G96-lipid.itp combination, I created a tutorial that teaches
you how to build the system and properly prepare the topology. It is
linked from the Tutorials page of the Gromacs site.
-Justin
Thank you in advance,
Christopher
--
========================================
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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