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.