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.
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 <[email protected]> > > > 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 | (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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