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 Thanks again, James 2012/6/8 Justin A. Lemkul <[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 | (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> >
-- 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
