[gmx-users] Coordinate file for lipid bilayer

[James Starlight]

Dear all!


Recently I've forced with the opposite problem. I have pre-equilbrated
bilayer of highter dimensions than I need. How I could reduce lipid number
of such bilayer as well as reduce total dimensions of such system ?

E.g I have preequilibrated bilayer consisted of 340 lipids. I want to
reduce it to the 200 lipids by the symmetrical deletion of the unnecessary
lipids from each side. Is there simplest way to do it ?

James

2012/5/28 Jon Kapla <jon.kapla at mmk.su.se>

>  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>
>
>> 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
>> (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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