[gmx-users] Charmm27 ff for membrane protein simulation

[James Starlight]

Thomas, Justin thank you for that information


Recently I've alredy tried to investigate CHARMM36 ff. I found that
lipid.rtp of that ff consist of data for different DPP lipids. But in those
DPPC lipid bilayer that I've used in the Justin's tutorial consist of 50
atoms for each monomer. In contrary the DPP lipids in the CHARMM ff consist
of more atoms and has another atom difinition.

E.g If I've tried to load my dppc.pdb to the pdb2gmx I've obtained error
that
Residue 'DPP' not found in residue topology database

Where I could find already preequilibrated bilayers adapted for the CHARMM
ff?


James

2011/10/18 Thomas Piggot <t.piggot at soton.ac.uk>

> By default in the CHARMM27 force field files there is no DPPC, as this is
> made up from a combination of other entries in the rtp file (because this is
> the way it is done in the CHARMM program's files). If you wish to use DPPC
> you can construct yourself a complete DPPC rtp entry. To do this you it is
> probably easiest to duplicate the DMPC entry and add the corresponding atoms
> and bonds for two extra carbons in each tail.
>
> Alternatively you could use the CHARMM36 force field (available to download
> from the contributions section of the website), there should already be an
> entry for DPPC.
>
> Cheers
>
> Tom
>
>
> On 18/10/11 19:45, Justin A. Lemkul wrote:
>
>>
>> James Starlight wrote:
>>
>>> Greetings!
>>>
>>>
>>> Recently I've found that Charmm27 ff is widely used for the simulation
>>> of the membrane proteins. I've tried to work with pure DPPC bilayer in
>>> pdb2grx and obtain that charm27 ff included in the Gromacs is lack for
>>> the parametries for the lipids.
>>>
>>> Could you tell me where I could obtain those parametries ( and tutorial
>>> of how it might be included in processing of lipids) or full functional
>>> charmm27 ff that already has pre-built those parametries?
>>>
>>>  Most of the common lipids are already present in lipids.rtp in
>> charmm27.ff in
>> Gromacs 4.5.x; if you are looking for lipids not present there, please be
>> more
>> specific as to what you need.
>>
>> The only membrane protein tutorial to my knowledge is my own.  Dealing
>> with
>> CHARMM should be significantly easier, however, as no modification of the
>> force
>> field is necessary.  Run pdb2gmx on a single lipid molecule, convert the
>> .top to
>> .itp (see the wiki) and #include it in the .top for your protein, just
>> like in
>> my tutorial.
>>
>> -Justin
>>
>>  Thank you for help
>>>
>>>
>>> James
>>>
>>>
> --
> Dr Thomas Piggot
> University of Southampton, UK.
>
>
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