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 <[email protected] <mailto:[email protected]>>
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
[email protected] <mailto:[email protected]> | Birmingham
AL 35294-4461
(205) 690-0808 |
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_____________________________________________________
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