Justin,
I've also look for the cap editing in the pymol but it seems that that function lacks in that program By the way, what are specificity of such Cap groups ? Do they are only sheld charges on the termi or have something addition function? What difference beetwen different caps I cant understand why in my structure there are so non-standart groups. James 2011/11/9 Justin A. Lemkul <jalem...@vt.edu> > > > James Starlight wrote: > >> Justin, >> >> Could you tell me another alternative ways to replace existing cap groups >> in my pdb besides xleap ? ( I've had many problems with the pdb's >> processed by this soft). Also I've tried to make topology for the >> non-standart caps by PRODRG but I also have some problems with such >> parametrisation. >> >> > Unless you describe your problems, there's very little anyone can or will > try to do to help you. I've never had a problem with an xleap coordinate > file, so I can't offer you any additional guidance with that. Otherwise, > there are dozens of programs that are capable of drawing molecules or > editing files. See, for instance: > > http://www.gromacs.org/**Documentation/File_Formats/** > Coordinate_File#Sources<http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources> > > -Justin > > >> Also I've not found suitable topology for some D-isomers ( it's strange >> that parametriation for such typical non-standart residues is absent in all >> force fields ). As I understood I cant use topology of L-analogs for the >> parametrisation of such D-forms because I dont know suitable parameters for >> dihedrals for instance. >> Have someone pre-built parameters for the D-aa for Gromos or Charmm force >> field? >> >> >> Thanks, >> >> James >> >> 2011/10/29 Justin A. Lemkul <jalem...@vt.edu <mailto:jalem...@vt.edu>> >> >> >> >> >> James Starlight wrote: >> >> Justin, hello! >> >> Could you tell me what exactly program from the Amber tools >> package you've used for the KALP peptide preparation e.g for >> capping ? >> >> >> xleap >> >> At this point, please start a new thread for your questions, as >> these topics are completely unrelated to where you started. >> >> -Justin >> >> >> -- ==============================**__========== >> >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> 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. 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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