[gmx-users] membrane model

[Justin Lemkul]

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
>>
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================