[gmx-users] RE: .rtp libraries lipids...
David van der Spoel
spoel at xray.bmc.uu.se
Mon May 17 10:11:17 CEST 2010
On 5/17/10 9:51 AM, lloyd riggs wrote:
> Dear All,
> This is a follow up on a post last week. I was trying to find pre-made .rtp libraries to add on for membrane lipids (other than DOPC, etc...). My critique was the complexity of membrane lipids means for most real processes we need to have a synthetic membrane (s) that reflect real life more acurattly, but figured people do not want to share their libraries for obvious reasons, etc...
The reason there are no such libraries is that pdb2gmx can not handle
these easily, since it is made for proteins. The main problem is that
such molecules do not usually have the same atom names in all coordinate
files, and this is what pdb2gmx relies on. You can find lipid topologies
on Peter Tieleman's website (itp files).
Of course if someone would provide lots of different coordinate files
and rtp files this could work in combination, but not for arbitrary lipids.
> In any case I could not find the exact review article, which lists similar figures and tables as below for most cells, and membranes within cells, but it is similar to this article...
> Lipid Composition of Cultured Murine Keratinocytes
> Kathi C Madison, Philip W Wertz, John S Strauss and Donald T Downing
> Stephan Watkins
David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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