[gmx-users] Pre-equilibrated CHARMM lipid bilayers

[James Starlight]

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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