Mark, Justin, Thanks for advises. Indeed I think that simple text editor would be better sollution in my casw because of small number of restraints.
I just have a question about definition of the Distances This is the default of the restraints between atom 10 and 16. [ distance_restraints ] ; ai aj type index type' low up1 up2 fac 10 16 1 0 1 0.0 0.3 0.4 1.0 I'd like to restrict distance between both of that atoms 7.96 < r(Ca-Ca)< 8.41 I've found that the up1 is the 7.96 and up2 is the 8.41 but how I could specify 'low' in the above table ? Should I obtain value for the initial Ca-Ca distance between my residues from the initial structure? How I could do it? James 12 марта 2012 г. 18:38 пользователь Justin A. Lemkul <jalem...@vt.edu>написал: > > > James Starlight wrote: > >> Francesca, >> >> Yes I suppose this is good aproach for the generation of position >> restricktions on the desired atoms. But I want to restrain the distance >> between selected pairs of atoms ( e.g between C-alpha- C-alpha atoms of two >> different residues). >> >> > How many restraints do you need to create? If they are this simple, you > can write them yourself using a text editor in conjunction with manual > section 4.3.4. Using genrestr is only really helpful when you require a > network of distance restraints between the atoms of a given group. If > there are only a few to create, it's actually more work to use make_ndx and > genrestr than it is to fire up your favorite text editor. > > > Also I want to restrain some dihedral angles in the desired rotameric >> forms. >> >> > See manual section 4.3.3 and http://www.gromacs.org/** > Documentation/How-tos/**Dihedral_Restraints<http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints> > . > > > In literature I've found that peple have dome the same things in Gromacs >> but I could not find detailed algorithm of such methodology :( >> >> > All relevant equations are provided in the manual, and examples are > provided either there or on the Gromacs site. If you need further > information, ask a specific question related to what you can't find or > don't understand. > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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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