2) Secondly the paper uses and validate many things with "S" configuration
DMPC bilayer (the single residue is in "S" configuration, as provided in
Richard's Bryce website). So can I assume these validations remain same for
"R" configurations as DMPC lipid is R (I dont have reference for that
though, but what CHARMM-GUI provides and other lipids are in R form only.).
So is there any special reason 'S' lipid was used in such study? Anyhow I
can use params for R also.
I assume you're talking about the stereogenic center of the phospholipid
(the sn-1 carbon) here. I believe for glycerophospholipids this is usually
in the R configuration (J. A. Smith Organic Chemistry).
As a side note, it is important to note that phosphatidylglycerol has
another chiral center, but only the S configuration occurs in nature (K. K.
Eklund et al. Biochemistry 1987).
3) Few lipids are there now in lipid11 (that charmmlipid2amber.x uses). As
far I was following recent archive mails AMBER will provide params which can
be used without surface tension once it is published. So the params in
lipid11 will change after it is published or these are same params which can
be used without surface tension?
Actually, many of the CHARMM-GUI lipids are supported with Lipid11. Lipid11
is a modular force field, so it supports many different combinations of head
groups and tail groups. See the Amber manual for a current list. However,
myristoyl was not included in the first version of Lipid11. Because we are
also interested in myristoyl, I am working on adding myristoyl to the
parameter set.
Currently, the Lipid11 parameters require a surface tension ensemble.
Running bilayer systems with Lipid11 and a tensionless ensemble does not
fully capture several experimental structural and dynamical properties. The
surface tension ensemble with this parameter set approximates the bilayer
behavior better for now.
However, we are continuing to refine and test parameters that will be
published in the future. These have not been released yet, but will be the
next version of the Amber lipid force field included in AmberTools.
Ben Madej
Walker Molecular Dynamics Lab
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Received on Fri Jul 13 2012 - 12:30:02 PDT
