[gmx-users] Coordinate file for lipid bilayer

[James Starlight]

Peter,

Thanks for advise.

I've found already pre-equilibrated POPC bilayers with 200 lipids. I've
examined that lipids and found that they are very similar to the berger's
lipids (it consists of equal nymber of atoms ) but the atom order in each
lipid is slightly different than in Tieleman's popc.itp file so during
processing of that lipids I've got error of non-matching atoms. Is there
any trivial way to make new popc.itp based on existing gro file with
correct atom order ?


James

2012/5/26 Peter C. Lai <pcl at uab.edu>

> Either use genbox -cs popc128b.gro or genconf -f popc128b.gro -nbox x y 0
> Tieleman's lipids require you to generate a dummy tpr for use with trjconv
> to unwrap the pbc (trjconv -s em.tpr -f popc128b.pdb -o popc128b-nopbc.gro
> -pbc mol -ur compact) first.
>
> Lots of people have their own bilayer but they may be for different FFs
> which means the atom naming would not be immediately be compatible with
> your FF; for example mine are built for charmm36 and would require atom
> renaming for another FF, even charmm27.
>
> On 2012-05-26 11:24:12AM +0400, James Starlight wrote:
> > Dear Gromacs Users!
> >
> >
> > I want to perform MD simulation of my membrane protein in POPC or POPE
> > bilayer using Tieleman's parameters for lipids by means of gromos united
> > atom force field. The main problem is that the pre-equilibrated bilayers
> > wich I found on the Dr. Tieleman's site consist of no more that 128
> lipids
> > but I want to simulate my protein with bigger number of lipids ( for
> > example starting from 200 lipids ).
> >  What should I do in that case ?  Could you provide me with  some tools
> for
> > construction of such united-atoms bilayers with desired dimensions ?
> > Finally is there any others pre-equilibrated bilayers aviable for
> > downloading besides Dr. Tieleman's site ?
> >
> >
> > thanks for your help,
> >
> > James S.
>
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> ==================================================================
> Peter C. Lai                    | University of Alabama-Birmingham
> Programmer/Analyst              | KAUL 752A
> Genetics, Div. of Research      | 705 South 20th Street
> pcl at uab.edu                     | Birmingham AL 35294-4461
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