[gmx-users] membrane model

[Thomas Piggot]

Well, the CHARMM ff is not entirely all-atom:

http://pubs.acs.org/doi/abs/10.1021/jp410344g

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). 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.