Hi Johnny, If for a dihedral the definition only lists two atoms, these signify the central atoms with any possible substituents. I think this is explained in Chapter 5 of the manual.
Cheers, Tsjerk On Sun, May 24, 2009 at 5:58 PM, Zhanglin Ni <z...@u.washington.edu> wrote: > The reason I asked the question was becuase I was trying to understand them > in order to parameterize some bonds myself. > for example, dihedral angles a lot time are clearly commented, so I know > which bonds could use the parameter. > e.g. > #define gd_4 180.000 5.86 1 > ; N-CHn-CHn-OA (lipid) 1.4 > ; > #define gd_5 180.000 9.35 1 > ; OA-CHn-CHn-OA (sugar) 2.2 > > But those like following is comfusing to me which conditions they are > discribing since it commented 2 atoms for a dihedral angle > #define gd_38 0.000 0.0 4 > ; -NR-FE- 0.0 > ; > #define gd_39 180.000 1.0 6 > ; -CHn-N,NE- 0.24 > ; > #define gd_40 0.000 1.0 6 > ; -CHn-C,NR(ring), CR1- 0.24 > ; > > > thanks > Johnny >> >> Message: 5 >> Date: Sun, 24 May 2009 16:42:35 +1000 >> From: Mark Abraham <mark.abra...@anu.edu.au> >> Subject: Re: [gmx-users] question about force field parameter >> To: Discussion list for GROMACS users <gmx-users@gromacs.org> >> Message-ID: <4a18ec5b.6060...@anu.edu.au> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> >> Zhanglin Ni wrote: >>> >>> Dear all >>> I am a little confused with some force field parameter library. for >>> example >> >> Whether and how this makes sense depends on the context, which you need >> to tell us, since we are not going to go looking and guessing for you. :-) >> >>> #define gd_26 0.000 2.93 3 >> >> This defines a preprocessor macro called gd_26 that replaces each >> instance of that token string with the three numbers above. >> >>> ; -CH2-S- 0.7 >> >> This is a comment line. >> >>> dihedral is supposed to be i j k l 4 atoms , why, for example, the case >>> above has only 2 atoms. >> >> You may need to consider the effect of that macro in the context where >> it is used. >> >> Mark >> >> >>> > > _______________________________________________ > gmx-users mailing list gmx-us...@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
