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 <jmsstarli...@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.pig...@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. >> >> >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> Please search the archive at http://www.gromacs.org/** >> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before >> posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read >> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> > >
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