[gmx-users] All-atom topologies for lipid head groups

[Thomas Piggot]

Hi,

A force file like this does exist 
(http://pubs.acs.org/doi/abs/10.1021/jp800687p) but be aware, like the 
CHARMM27 force field it is based upon, you will need to use 
surface-tension to keep these lipids in the correct phase.

Cheers

Tom

Justin A. Lemkul wrote:
> 
> Ioannis Beis wrote:
>> Dear Gromacs users,
>>
>> I am a new user and I am trying to study the physical properties of the 
>> interactions between cytosolic proteins and lipids. I have created the 
>> Berger-Gromos combination, as described by Mr. Justin Lemkul in his 
>> KALP15 in DPPC tutorial, as well as Berger-OplsAA, as described by Mr. 
>> Chris Neale in gromacs mailing list. All-atom topologies might turn out 
>> to be crucial in my work, both in the results and the data analysis 
>> (e.g. H-bonds).
>>
>> Even if the all-atom model of Opls-AA is used for the proteins, the 
>> lipid head groups would still have a united-atom description and 
>> therefore the interactions can't be treated in an all-atom level.
>>
>> I thought of creating a new topology for the lipid head groups under a 
>> head.itp file, by using parameter values from Dundee server and/or 
>> Opls-AA, even though I do not know yet exactly how and I feel very 
>> unsure about the eventual incorporation into the Berger-OplsAA 
>> combination. Then taking single lipids of pre-equilibrated membranes, 
>> editing accordingly the coordinate file (i.e. replacement of polar head 
>> atoms and use of new coordinates, names and residue names for them) and 
>> subsequently building bilayers.
>>
>> I would really appreciate if someone could send suggestions. In 
>> addition, if someone already has an all-atom description of lipid 
>> head-groups compatible with a protein-membrane force field combination 
>> with all-atom protein description, I would be grateful if he/she could 
>> share.
>>
>> Thank you in advance.
>>
> 
> It sounds to me like you're trying to create a Frankenstein force field.  Why 
> wouldn't a UA representation of the lipids work?  For hydrogen bonding, all 
> polar groups are represented with explicit H atoms.  This is generally true of 
> all UA force fields, for lipids and proteins alike.
> 
> If you really want an AA representation of your molecules, you're probably 
> better off just applying the CHARMM force field to the whole system.  The latest 
> version of Gromacs supports CHARMM, which includes a number of common lipids.
> 
> -Justin
> 

-- 
Dr Thomas Piggot
University of Southampton, UK.