Justin? So As I understood the aminoacids.rtp of current force field must include topology for such caps.
But for example If I have only topology on such groups for another ff could I include it to the amber FF? If no where I could find such topology ? James 2011/10/28 Justin A. Lemkul <jalem...@vt.edu> > > > James Starlight wrote: > >> >> I understood that but how I can add that groups to termi of the bowh of my >> chains ? >> >> I've tried by -ter but pdb2gmx didnt ask me for the addition of the CAPS. >> May be Amber ff didnt support this feature ? >> >> > pdb2gmx does not build things that aren't there. Your input coordinate > file needs to have the capping groups present, with all atoms named as the > .rtp entries expect them, hence the suggestion to investigate the [ACE] and > [NME] directives. > > -Justin > > > >> James >> >> >> You have to build capping groups onto the termini. See, for >> instance the [ACE] and [NME] groups in the .rtp file. >> >> -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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