[gmx-users] Coordinate file for lipid bilayer

[Jon Kapla]

Hi,

The easiest solution is probably to write a script that reorders the 
structure file (gro for example, just swap the lines in each lipid, and 
use "editconf -f file.gro -resnr 1"  to renumber) the way it is written 
in the topology.

Cheers
Jon

On 2012-05-28 08:03, James Starlight wrote:
> 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 <mailto: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 <mailto:pcl at uab.edu>                     | Birmingham
>     AL 35294-4461
>     (205) 690-0808                  |
>     ==================================================================
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-- 
_____________________________________________________

Jon Kapla
   Division of Physical Chemistry
   Dpt. of Materials and Environmental Chemistry (MMK)
   Arrhenius Laboratory
   Stockholm University
   SE-106 91 Stockholm
Pos:    PhD Student
Phone:  +46 8 16 11 79 (office)
Phone:  +46 70 304 19 89 (cell)
E-mail: jon.kapla at mmk.su.se
_____________________________________________________

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