[gmx-users] POPG-Martini Force Field

[XAvier Periole]

On Oct 23, 2009, at 9:45 AM, Amit Choubey wrote:

>
>
> On Fri, Oct 23, 2009 at 12:33 AM, XAvier Periole <x.periole at rug.nl>  
> wrote:
>
> On Oct 22, 2009, at 11:28 PM, Amit Choubey wrote:
>
>>
>>
>> On Thu, Oct 22, 2009 at 9:53 AM, S hv <solar30 at hotmail.com> wrote:
>> Hi,
>>
>> I am currently working with peptide/lipids interactions using the  
>> martini force field. I want to built a bacterial membrane, so I  
>> trying to find the
>> topology of the POPG lipid but until now without success.
>>
>>
>> In the martini_v2.0_lipids.itp file, the PG lipids are no included.  
>> I have seen some works using the martini force field and POPG  
>> lipids, e.g., " The molecular mechanism monolayer PNAS 105,  
>> 10803-10808", but they don't specify the topology of POPG lipids.
>>
>> You can do this on your own just pull out the atomic structure of  
>> DPPC and POPG from any website. Compare atomistic DPPC with the  
>> Coarse Grained DPPC and it wont be hard to figure out the POPG CG  
>> topology.
> That is certainly not that easy. A lot of parameterizations efforts  
> have to be
> involved.
>
> No, thats easy because you are working with a coarse grained model.  
> There are are only few types of particles possible. The only tricky  
> ones are the head groups which the paper does mention.
If the bead type is given in the paper then the work is easier.
My point is that assimilate CG with simple is a big mistake!
>
>>
>> BTW, the paper does give a short description about the topology of  
>> POPG
> The best is probably to ask the authors of that paper to share their  
> topology,
> which they should.
>>
>>
>> I also tried in the martini web page, but I just found the  
>> martini_v2.0_lipids.itp file.
>>
>> Could anyone help me to find such topology?
>>
>> Thanks a lot for your time,
>>
>> Salvador
>>
>> Windows Live: Make it easier for your friends to see what you’re up  
>> to on Facebook.
>>
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