[gmx-users] DPPC-DOTAP Mixed Lipid Bilayer

[Tsjerk Wassenaar]

Hi Nidhin,

It looks like you have a version of insane that still builds oleyl with
five beads. It should be four as 'CDCC' like you did for building the
topology. So you also need to remove the C5 beads and shift the D to
position two. Then you should be set to make/simulate your bilayers.

Cheers,

Tsjerk
On Jun 8, 2016 6:47 AM, "Nidhin Thomas" <nidhin.thomas0624 at gmail.com> wrote:

> Hi Dr. Wassenaar,
>
> I have edited insane.py using the following command.
>
> "DOTAP": (moltype, " -   -   -   -   -  NC3 GL1 GL2 C1A C2A D3A C4A C5A
> -  C1B C2B D3B C4B C5B  - “),
>
> I replaced NC3 of DOPC with ‘-‘ and PO4 of DOPC with NC3 as you suggested.
> Then I used insane.py to create the mixed bilayer of DPPC-DOTAP.
>
> I also created the .itp file for DOTAP using lipid-martini-itp.py code.
>
> I used the command given below to create the .itp file.
>
> python lipid-martini-itp.py -o martini_v2.0_DOTAP_01.itp -alname DOTAP
> -alhead 'C' -allink 'G G' -altail 'CDCC CDCC’
>
> Is this the correct method to create the bilayer and .itp file? Is there
> anything more that I should do?
>
> Thanks a lot for helping me to create the bilayer.
>
> Regards,
>
> Nidhin Thomas
> University of Houston
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