[gmx-users] Pre-equilibrated CHARMM lipid bilayers

[Peter C. Lai]

I am not 100% sure how the differences in c36 will affect the parameters you
get from SwissParam.

Personally I prefer to use ParamChem (CHARMM's version of Swissprot) to
give me ligand parameters using CGenFF atomtypes, since I have CGenFF 
merged into my Charmm36 forcefield in gromacs.
 

On 2012-12-19 10:37:40AM +0300, James Starlight wrote:
> Peter, many thanks!
> 
> 
> Could you tell me is there any differences in atom types between
> charmm27 and charmm36 ff? I'd like to simulate receptor-ligand complex
> in that bilayer where ligand molecule would be parametrized by
> Swiss-param ( make topology for the ligands in charmm27 ff). So
> because receptor and bilayer will be parametrized in charmm36 I'm not
> sure about proper working of Swiss's topology with that complex.
> 
> James
> 
> 2012/12/19 Peter C. Lai <pcl at uab.edu>:
> > http://cesium.hyperfine.info/~peter/gromacs/popc36/
> > has a fully gromacs compatible charmm36 238 POPC bilayer with 21524 waters
> >
> > On 2012-12-18 09:07:22PM -0800, James Starlight wrote:
> >> Justin, thanks again.
> >>
> >> As I understood gromacs already had had parameters for charmm lipid so
> >> the main approach is to do ITP file for 1 lipid by means of pdb2gmx
> >> isnt it?
> >>
> >> By the way is there any way to convert PSF or CRD file to PDB?
> >>
> >> I've found suitable bilayer for my simulation but it lack such coordinates.
> >> POPE Bilayer (310.15K, A=65.2 Â/lipid, 10ns, 340 lipids, noLRCs):
> >> CHARMM PSF, X-Plor/NAMD PSF, and CHARMM CRD
> >>
> >> James
> >>
> >> 2012/12/18, Justin Lemkul <jalemkul at vt.edu>:
> >> >
> >> >
> >> > On 12/18/12 2:02 PM, James Starlight wrote:
> >> >> Dear Gromacs Users!
> >> >>
> >> >> I'm looking for 150-200 lipid bilayer ( POPC or POPE) parametrized in
> >> >> charmm27 or charmm36 force field and pre-equilibrated in NPT
> >> >> conditions. I'll bevery thankfull to anybody who provide me with the
> >> >> coordinates as well as itp file for such bilayer.
> >> >>
> >> >
> >> > http://terpconnect.umd.edu/~jbklauda/research/download.html
> >> >
> >> > Google is your friend.  There are plenty more places to look.  A search for
> >> >
> >> > "POPC CHARMM membrane coordinates" (without the quotes) does the trick.
> >> >
> >> > -Justin
> >> >
> >> > --
> >> > ========================================
> >> >
> >> > Justin A. Lemkul, Ph.D.
> >> > Research Scientist
> >> > Department of Biochemistry
> >> > Virginia Tech
> >> > Blacksburg, VA
> >> > jalemkul[at]vt.edu | (540) 231-9080
> >> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >> >
> >> > ========================================
> >> > --
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