Hi, If you poke your finger into something, it isn't going to stay flat. :-)
Mark On Wed, Jan 17, 2018 at 9:44 PM MD <refm...@gmail.com> wrote: > Hi Mark, > Can you tell me more details about the ring's atoms interacting with an > environment? What interactions did you mean? > Thanks, > Ming > > On Tue, Jan 16, 2018 at 6:43 AM, Mark Abraham <mark.j.abra...@gmail.com> > wrote: > > > Hi, > > > > You still have many sources of problems (e.g. the warnings you > suppressed, > > the fact that your ring's atoms interact with an environment). What > happens > > when you minimize a capped peptide in vacuo? > > > > Mark > > > > On Tue, Jan 16, 2018 at 12:39 PM MD <refm...@gmail.com> wrote: > > > > > Hi Justin, > > > > > > I got the itp and parameters of my side chain modified amino acid from > > > CHARMM-GUI and incorporated it into my protein structure, labeled with > > > HETATM. I made the atom types names consistent with charmm forcefield > > which > > > I used with gromacs and made sure overall the parameters look decent > for > > > now. After some fixing the grompp would run with no warnings, and I > did a > > > quick energy minimization, but ended up with a distorted six member > > ring. I > > > have the picture and my parameters attached. Your time is appreciated > :) > > > > > > > > > https://docs.google.com/document/d/1bjSq55HDLRsSVGqm5i0MRwI- > > rgIesxy0QdIHm7tqTug/edit?usp=sharing > > > > > > Ming > > > > > > On Mon, Jan 15, 2018 at 7:53 PM, Justin Lemkul <jalem...@vt.edu> > wrote: > > > > > > > > > > > > > > > On 1/15/18 7:45 PM, MD wrote: > > > > > > > >> Hi Gromacs, > > > >> > > > >> I have a modified side chain amino acid and it has a six member ring > > > >> attached to it. Regarding this ring I had dihedral angles taken care > > > with > > > >> some 0s and some 180s. However, after minimization my structure > looks > > > very > > > >> strange, the ring is not flat and the dihedral angles in my settings > > > >> didn't > > > >> seem to apply to the minimized structure at all. Any thoughts? > > > >> > > > > > > > > You're going to have to provide a lot more detail. You're > parametrizing > > > > something nonstandard, so there are plenty of places to make > mistakes. > > > > Without knowing your structure, the actual parameters and how derived > > and > > > > validated them, there's nothing to do but guess. > > > > > > > > Keep in mind that rings are not necessarily perfectly planar, and the > > > > values set for dihedral phase offsets do not strictly mean the values > > > that > > > > the dihedrals must adopt. > > > > > > > > -Justin > > > > > > > > -- > > > > ================================================== > > > > > > > > Justin A. Lemkul, Ph.D. > > > > Assistant Professor > > > > Virginia Tech Department of Biochemistry > > > > > > > > 303 Engel Hall > > > > 340 West Campus Dr. > > > > Blacksburg, VA 24061 > > > > > > > > jalem...@vt.edu | (540) 231-3129 > > > > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html > > > > > > > > ================================================== > > > > > > > > -- > > > > Gromacs Users mailing list > > > > > > > > * Please search the archive at http://www.gromacs.org/Support > > > > /Mailing_Lists/GMX-Users_List before posting! > > > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > * For (un)subscribe requests visit > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at http://www.gromacs.org/ > > Support/Mailing_Lists/GMX-Users_List before posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
