[gmx-users] Charmm27 ff for membrane protein simulation

[James Starlight]

It seems very strange but i could not find such parameters for charmm
lipids :( only berger lipids are presented on the world wide :D

I've another question about conversion of the topology formats

e.g I have topology and parameters for some molecules written for CHARMM
program in file .rtf and .prm file formats respectively
could I convert this topology  to the gromacs standart .rtp or .itp
topology ? How I could adapt parameters in .prm for gromacs ?


James

2011/10/19 James Starlight <jmsstarlight at gmail.com>

> 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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