[gmx-users] Simultaing protein, water and lipid together

Justin A. Lemkul jalemkul at vt.edu
Wed Mar 17 11:54:35 CET 2010

radhika jaswal wrote:
> Hi Everyone there....
> I want to simulate peptide, water and few lipid molecules together...but 
> by all the possible sources i am just able to find the full dmpc or 
> dppc.pdb....not single molecule parameters of any single lipid molecule...
> All sugestions are welcome.

Your question is not well-formed.  Do you just need the coordinates of a single 
lipid from, for example, a pre-equilibrated membrane?  If so, just use a text 
editor to pull one out.  Do you need parameters for this lipid?  Note that .pdb 
files do not contain parameters, they contain coordinates.  Most standard lipids 
can be found at several sites, most commonly Peter Tieleman's.

In any case, I'd suggest that you have a look at the membrane protein tutorial 
linked on the Gromacs site.  Even if you don't want to work with a whole 
membrane, many of the same issues will come up, as far as setting up the system 


> Thanks
> Radhika
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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