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 <[email protected]> > > > 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 <[email protected] <mailto:[email protected]>> >> >> >> >> >> 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 [email protected] <mailto: >> [email protected]> >> >> 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 [email protected] >> <mailto:gmx-users-request@**gromacs.org<[email protected]> >> >. >> 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 [email protected] > 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 [email protected]. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
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