Peter,
so as I understood after the integration of the CGenFF params into the charm36 rtp ligand ( in complex with the protein) might be parametrized just by pdb2gmx. Does this correct ? James 2012/12/20 Peter C. Lai <[email protected]>: > 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 <[email protected]>: >> > 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 <[email protected]>: >> >> > >> >> > >> >> > 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 [email protected] >> >> > 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 [email protected]. >> >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> > >> >> -- >> >> gmx-users mailing list [email protected] >> >> 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 [email protected]. >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > >> > -- >> > >> > -- >> > gmx-users mailing list [email protected] >> > 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 [email protected]. >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> -- >> gmx-users mailing list [email protected] >> 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 [email protected]. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- > > -- > gmx-users mailing list [email protected] > 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 [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
