Justin I have one extra question about parametrisation of the bond type
Initially I had -c-c- bond so both atoms were in the sp3 hybridization. I've changed bond type between that atoms to the gb_16 ( from phe ring) to define them as the >c=c< but during the simulation I've noticed that the bond between that atoms is not planar ( sp2 form) and still is in the sp3. What addition changees should I do in my topology to change the planarity of new bond ? Should I make some changes ia angles term as well? E.g I've found 612 613 614 2 ga_13 ; where 612 and 613 are the atoms wich I would like to present as the rigid. I've change to the ga_27 ( 120) but during simulation the bond was still in sp3. What I've done wrong ? James 2012/6/8 James Starlight <jmsstarli...@gmail.com> > Justin, > > > > thanks alot. I'll try to use gb_10 ( for C=N) as well as gb_16 ( for C=C) > for parametrisation in my task. > > > > James > > 2012/6/8 Justin A. Lemkul <jalem...@vt.edu> > >> >> >> On 6/8/12 2:01 PM, James Starlight wrote: >> >>> Justin, >>> >>> Does the gb_10 suitable for both bonds that I want to parametrise ? >>> >>> As I've told previously I need to parametrise two different bonds >>> >>> 1) is the >C=C< bond wich are not in the ring. This is just double bound >>> in >>> linnear sequence -C=C-. >>> >>> 2) is the >C=N- double bond where both atoms in the 5-m ring system >>> >>> >> This is a better description. The last message suggested everything was >> in a 5-membered ring. Had that been the case, my suggestion would have >> been right (see, for instance, a HIS side chain - gb_10 is used for both >> C=C and C=N in that case). >> >> There are no linear C=C bonds in Gromos force fields by default, as such >> groups are not in proteins. The closest you can likely come is to take a >> C=C bond from the PHE ring. Bond lengths are simple, and are usually >> derived from spectroscopic information. If using constraints on all bonds, >> the force constant is irrelevant since the bond is rigid. If not using >> constraints, then you'll have to find or derive suitable parameters >> yourself. Welcome to the inconvenient world of parameterization :) >> >> -Justin >> >> Thanks again, >>> >>> James >>> >>> >>> >>> 2012/6/8 Justin A. Lemkul <jalem...@vt.edu <mailto:jalem...@vt.edu>> >>> >>> >>> >>> >>> On 6/8/12 1:22 PM, James Starlight wrote: >>> >>> I've found that information in ffbonded.itp but I'm not sure >>> about exactly >>> meaning of some types. >>> >>> >>> E.g I'm looking for bond type for simple double bond between C=C >>> as well >>> as C=N >>> ( here both atoms in 5-m ring) atoms pairs. Should I use for the >>> first one >>> #define gb_15 0.1390 8.6600e+06 >>> ; CH2 - C, CR1 (6-ring) 800 >>> >>> and for the second one ; >>> >>> #define gb_11 0.1340 1.0500e+07 >>> ; C - N, NZ, NE 900 >>> ? >>> >>> >>> Neither. gb_10 sounds exactly like what you need: >>> >>> #define gb_10 0.1330 1.1800e+07 >>> ; C, CR1 - N, NR, CR1, C (peptide, 5-ring) 1000 >>> >>> -Justin >>> >>> -- >>> ==============================**__========== >>> >>> >>> Justin A. Lemkul, Ph.D. >>> Research Scientist >>> Department of Biochemistry >>> Virginia Tech >>> Blacksburg, VA >>> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >>> >>> http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin> >>> >>> <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >>> > >>> >>> ==============================**__========== >>> >>> -- >>> gmx-users mailing list gmx-users@gromacs.org <mailto: >>> gmx-users@gromacs.org> >>> >>> http://lists.gromacs.org/__**mailman/listinfo/gmx-users<http://lists.gromacs.org/__mailman/listinfo/gmx-users> >>> >>> >>> <http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>> > >>> Please search the archive at >>> >>> http://www.gromacs.org/__**Support/Mailing_Lists/Search<http://www.gromacs.org/__Support/Mailing_Lists/Search> >>> >>> >>> <http://www.gromacs.org/**Support/Mailing_Lists/Search<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 >>> <mailto:gmx-users-request@**gromacs.org<gmx-users-requ...@gromacs.org> >>> >. >>> Can't post? Read >>> http://www.gromacs.org/__**Support/Mailing_Lists<http://www.gromacs.org/__Support/Mailing_Lists> >>> >>> <http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>> > >>> >>> >>> >> -- >> ==============================**========== >> >> 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<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<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> Please search the archive at http://www.gromacs.org/** >> Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> >> > >
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