[gmx-users] topologies for POPE and DMPE

[Thomas Piggot]

Hi Pramod,

Please keep all general queries and questions on the GROMACS mailing list.

For CHARMM27, POPC can be found as an rtp entry. This means a topology 
can be generated using pdb2gmx. It is easiest if you do this using one 
POPC lipid and then make an itp from the top. A CHARMM POPC bilayer can 
be downloaded from the internet 
(http://terpconnect.umd.edu/~jbklauda/research/download.html).

Cheers

Tom

ram bio wrote:
> Dear Dr.Tom,
> 
> This is in response to the your message regarding the lipid bilayers
> for MD simulation. I have a protein and ligand complex to be simulated
> in lipid bilayer. Do, you have POPC structure and itp files
> parameterised by CHARMM 27 FF.
> 
> Regards,
> 
> Pramod
> 
> On Mon, Oct 17, 2011 at 12:07 PM, Thomas Piggot <t.piggot at soton.ac.uk> wrote:
>> Hi Roy,
>>
>> PE lipids are less frequently used than PC ones and there are fewer
>> topologies available. Also it has been shown that using the Berger PC lipid
>> topologies (the most frequently used united-atom PC lipids) and simply
>> changing the CH3 atoms in the head group to H is not a good approach for PE
>> (de Vries et al. DOI: 10.1021/jp0366926 is I think the first mention of
>> this).
>>
>> Other PE topologies I am aware of are either the all-atom CHARMM (27 or 36)
>> lipids or there are two united-atom GROMOS PE topologies:
>>
>> The first is the GROMOS43A1-S3 force field which has a POPE topology (you
>> can download this from the contributions section on the GROMACS website). I
>> have simulated a POPE membrane using these parameters before with no
>> problems.
>>
>> The second (and here is a shameless plug for some of my work, sorry!) is a
>> GROMOS53A6 based PE described in a paper we have just got accepted into J.
>> Phys. Chem B (http://dx.doi.org/10.1021/jp207013v). The supplementary
>> information for this paper (which is not yet available) has an
>> analysis/validation of POPE and DPPE membrane using these parameters which
>> are based upon the PC topologies of Kukol (DOI: 10.1021/ct8003468) and
>> Chandrasekhar (DOI: 10.1007/s00249-002-0269-4). If you (or anyone else) wish
>> to use these PE topologies send me an email off-list and I can let you have
>> them. I have not tested DMPE yet but I would imagine it should be similar to
>> DPPE and you can also make a DMPE bilayer from a DPPE one by simply removing
>> two CH2 groups from each lipid tail and equilibrating the new membrane.
>>
>> Cheers
>>
>> Tom
>>
>> Roy Lee wrote:
>>> Dear all,
>>>
>>>
>>> I would like to simulate my protein in a lipid bilayer using gromacs
>>> 4.5.4, and a forcefield of gromos96. However i don't have the topologies
>>> files for lipid bilayer for POPE and DMPE. Anybody knows where can i get the
>>> topologies file for POPE and DMPE ?
>>>
>>>
>>> Any help is much appreciated.
>>>
>>>
>>> Thanks a lot!
>>>
>>>
>>> Roy
>>>
>> --
>> Dr Thomas Piggot
>> University of Southampton, UK.
>> --
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-- 
Dr Thomas Piggot
University of Southampton, UK.