[gmx-users] membrane model

[Thomas Piggot]

Good to see the membrane structures have been changed/fixed. I think it 
was December 2010 when I last downloaded the POPC one!

I did port over the lipid parameters for C27-UA a good while ago but 
haven't got around to the C36-UA parameters yet.

On 19/06/15 16:55, Justin Lemkul wrote:
>
>
> On 6/19/15 11:38 AM, Thomas Piggot wrote:
>> Well, the CHARMM ff is not entirely all-atom:
>>
>> http://pubs.acs.org/doi/abs/10.1021/jp410344g
>>
>
> True, people have developed UA force fields from CHARMM's all-atom 
> models.  My comment was largely motivated by the fact that the 
> official CHARMM36 port for GROMACS is based entirely on all-atom 
> models.  If one wants to use CHARMM36-UA in GROMACS, the force field 
> parameters will have to be ported over.
>
>> As for downloading the structure, I would be slightly careful with 
>> the link that
>> Justin provided for POPC as (well, based upon the last time I used it 
>> anyway)
>> there were a different number of lipids in each leaflet of the 
>> membrane (65/63).
>
> That doesn't appear to be the case with either of the POPC membranes 
> currently available for download.  64 in each, at least according to 
> gmx select :)
>
> -Justin
>
>> Plus, you should also be aware that the topology on this site is not 
>> quite the
>> same as that described by Berger et al. If you are interested, see this
>> shameless plug to my own work for more details about this:
>>
>> http://pubs.acs.org/doi/abs/10.1021/ct3003157
>>
>> We had intended to make all our structures, etc. from this work 
>> available online
>> but never quite got around to it. If you need a particular structure, 
>> send me an
>> off list email and I can try and help.
>>
>> Finally, as for using the CHARMM-GUI, Justin is correct that it won't 
>> provide
>> you a united-atom membrane straight out of the box. However, a simple 
>> script can
>> be used to strip out the hydrogens and rename the atoms, should you 
>> really wish
>> to use it to build your membrane system (I have done this before for 
>> converting
>> DPPC/POPC membranes to a range of different united-atom force fields).
>>
>> Cheers
>>
>> Tom
>>
>> On 19/06/15 15:53, Justin Lemkul wrote:
>>>
>>>
>>> On 6/19/15 10:52 AM, anu chandra wrote:
>>>> Dear Gromacs users,
>>>>
>>>> I am planing to do a protein simulation in acyl chain united-atom POPC
>>>> membrane model. It will of great help if few of my queries regarding
>>>> setting up the system get answered.
>>>>
>>>> 1. Which force filed will be suitable for united atom (acyl chain) 
>>>> POPC?
>>>> Will CHARMM36 have united atom force filed for POPC?
>>>>
>>>
>>> No.  CHARMM36 is an all-atom force field.
>>>
>>>> 2. can somebody suggest me a site where I can get united atom membrane
>>>> model of POPC membrane?
>>>>
>>>
>>> http://wcm.ucalgary.ca/tieleman/downloads
>>>
>>>> 3. Will CHARMM-gui a good option for build the this particular system?
>>>>
>>>
>>> Not if you want a united-atom model.
>>>
>>> -Justin
>>>
>>
>

-- 
Dr Thomas Piggot
University of Southampton, UK.