[gmx-users] DPPC to CG DPPC

[sunny mishra]

Alright thanks. So should I do it for proteins?

On Tue, Dec 15, 2009 at 12:12 PM, XAvier Periole <x.periole at rug.nl> wrote:

>
> No need of position restrained simulation with the CG lipids.
> CG is very forgiving :))
>
> For proteins it is more delicate.
>
> On Dec 15, 2009, at 6:02 PM, sunny mishra wrote:
>
> Thanks for the reply. I have another quick question that If I have to do
> the Position Restrained EM Simulation of CG DPPC lipid then is it done the
> same way we do for atomistic structure of proteins like by defining the
> LIPPOSRES in the lipid.mdp file or while using MARTINI forcefield is there
> any other way of doing the Position Restrained EM simulation of CG DPPC
> lipids?
>
> On Tue, Dec 15, 2009 at 10:55 AM, XAvier Periole <x.periole at rug.nl> wrote:
>
>>  I have downloaded the 128 DPPC lipid molecules from Dr. Tielmen's Website
>>> and I am trying to convert the Atomistic structure to CG structure. For that
>>> I am using atom2cg script provided by the martini folks but it doesn't
>>> convert the Atomistic structure to CG structure. atom2cg script works well
>>> for converting the atomistic structure of PROTEIN to CG structure of protein
>>> but for LIPIDS it doesn't work. Does anyone know how can I convert the 128
>>> DPPC atomistic structure of lipids to CG structure.
>>>
>>>  This is correct. atom2cg is only working for proteins ...
>>
>> I would suggest you take dppc structure file from the martini web site!
>>
>>  Best Regards,
>>>
>>> Sunny
>>>
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