[gmx-users] gromacs.org_gmx-users Digest, Vol 146, Issue 33

[Nidhin Thomas]

Hi Dr. Wassenaar,

I will change insane.py accordingly and give a run.

Thanks a lot!

Regards,

Nidhin Thomas
University of Houston
> ------------------------------
> 
> Message: 4
> Date: Wed, 8 Jun 2016 06:52:27 +0200
> From: Tsjerk Wassenaar <tsjerkw at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] DPPC-DOTAP Mixed Lipid Bilayer
> Message-ID:
> 	<CABzE1SiqQD9w50p9o_gnt7HQWsvLA=hscf1g2ZKcceLvbqG9vA at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
> 
> 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
>> --
>> Gromacs Users mailing list
>> 
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>> 
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> 
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.