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 <p...@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 <jalem...@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 > >> > > >> > ======================================== > >> > -- > >> > gmx-users mailing list gmx-users@gromacs.org > >> > http://lists.gromacs.org/mailman/listinfo/gmx-users > >> > * Please search the archive at > >> > 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 > >> > > >> -- > >> gmx-users mailing list gmx-users@gromacs.org > >> http://lists.gromacs.org/mailman/listinfo/gmx-users > >> * Please search the archive at > >> 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 > > > > -- > > > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > > 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 > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > 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 -- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at 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