It seems very strange but i could not find such parameters for charmm lipids :( only berger lipids are presented on the world wide :D<br><br>I've another question about conversion of the topology formats<br><br>e.g I have topology and parameters for some molecules written for CHARMM program in file .rtf and .prm file formats respectively<br>
could I convert this topology to the gromacs standart .rtp or .itp topology ? How I could adapt parameters in .prm for gromacs ?<br><br><br>James<br><br><div class="gmail_quote">2011/10/19 James Starlight <span dir="ltr"><<a href="mailto:jmsstarlight@gmail.com">jmsstarlight@gmail.com</a>></span><br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">Thomas, Justin thank you for that information<br><br><br>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.<br>
<br>E.g If I've tried to load my dppc.pdb to the pdb2gmx I've obtained error that <br>Residue 'DPP' not found in residue topology database<br><br>Where I could find already preequilibrated bilayers adapted for the CHARMM ff?<br>
<font color="#888888">
<br><br>James</font><div><div></div><div class="h5"><br><br><div class="gmail_quote">2011/10/18 Thomas Piggot <span dir="ltr"><<a href="mailto:t.piggot@soton.ac.uk" target="_blank">t.piggot@soton.ac.uk</a>></span><br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
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.<br>
<br>
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.<br>
<br>
Cheers<br>
<br>
Tom<div><br>
<br>
On 18/10/11 19:45, Justin A. Lemkul wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
James Starlight wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Greetings!<br>
<br>
<br>
Recently I've found that Charmm27 ff is widely used for the simulation<br>
of the membrane proteins. I've tried to work with pure DPPC bilayer in<br>
pdb2grx and obtain that charm27 ff included in the Gromacs is lack for<br>
the parametries for the lipids.<br>
<br>
Could you tell me where I could obtain those parametries ( and tutorial<br>
of how it might be included in processing of lipids) or full functional<br>
charmm27 ff that already has pre-built those parametries?<br>
<br>
</blockquote>
Most of the common lipids are already present in lipids.rtp in charmm27.ff in<br>
Gromacs 4.5.x; if you are looking for lipids not present there, please be more<br>
specific as to what you need.<br>
<br>
The only membrane protein tutorial to my knowledge is my own. Dealing with<br>
CHARMM should be significantly easier, however, as no modification of the force<br>
field is necessary. Run pdb2gmx on a single lipid molecule, convert the .top to<br>
.itp (see the wiki) and #include it in the .top for your protein, just like in<br>
my tutorial.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Thank you for help<br>
<br>
<br>
James<br>
<br>
</blockquote></blockquote>
<br>
-- <br></div>
Dr Thomas Piggot<br>
University of Southampton, UK.<div><div></div><div><br>
<br>
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