I see, thanks for your help! On Wed, Apr 5, 2017 at 9:27 AM, Mark Abraham <mark.j.abra...@gmail.com> wrote:
> Hi, > > The protonation state is a decision you make in setting up the topology > (what pH am I modelling?). Having done so, you get whatever amine model the > force field specifies, and I expect that no force field has such a planar > amine, because none actually have the improper dihedral you suggest they > do, for the reason you suggest. :-) > > Mark > > On Wed, Apr 5, 2017 at 4:10 PM Phillip Rauscher <pmrausc...@uchicago.edu> > wrote: > > > Thanks so much for the reply Mark! For my own curiosity, is there a way > > that people generally deal with neutral sp3 Nitogens? They're chiral > > centers on simulation time scales, but on macroscopic scales pyramidal > > inversion eliminates that. > > > > On Wed, Apr 5, 2017 at 1:16 AM, Mark Abraham <mark.j.abra...@gmail.com> > > wrote: > > > > > Hi, > > > > > > Amide nitrogen atoms are trigonal planar because the group is planar. > > > There's no free rotation about the n-c bond, and the lone pair forms a > > > hybrid orbital with the carbonyl. > > > > > > Mark > > > > > > On Tue, 4 Apr 2017 18:05 Phillip Rauscher <pmrausc...@uchicago.edu> > > wrote: > > > > > > > It occurs to me that an example would be helpful. Here is an excerpt > > > from > > > > the OPLS aminoacids.rtp file detailing alanine: > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > *[ ALA ] [ atoms ] N opls_238 -0.500 1 H > opls_241 > > > > 0.300 1 CA opls_224B 0.140 1 HA opls_140 > > > > 0.060 1 CB opls_135 -0.180 2 HB1 opls_140 > > > > 0.060 2 HB2 opls_140 0.060 2 HB3 opls_140 > > > > 0.060 2 C opls_235 0.500 3 O opls_236 > > > > -0.500 3 [ bonds ] N H N CA CA HA CA > CB > > > > CA C CB HB1 CB HB2 CB HB3 C O -C N > [ > > > > impropers ] -C CA N H improper_Z_N_X_Y CA +N > > > > C O improper_O_C_X_Y * > > > > > > > > We can see that the Nitrogen is bound to atoms H, CA, and -C (on the > > > > previous residue). In the [impropers] section, an improper dihedral > is > > > > defined for these four atoms (with the nitrogen in both of the > dihedral > > > > planes). If we look at the definition of that improper in the OPLS > > > > ffbonded.itp file, we see the following: > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > *[ dihedraltypes ]; Improper OPLS dihedrals to keep groups planar.; > > (OPLS > > > > doesnt use impropers for chiral atoms).; Since these functions are > > > periodic > > > > of the form 1-cos(2*x), they are actually; implemented as proper > > > dihedrals > > > > [1+cos(2*x+180)] for the moment, ; to keep things compatible.; The > > > defines > > > > are used in ffoplsaa.rtp or directly in your .top file....; Z -N?-X > -Y > > > > improper torsion#define improper_Z_N_X_Y 180.0 4.18400 > 2* > > > > Given the functional form and the parameters used, this potential has > > > > minima at 0 and 180 degrees, thus keeping all four atoms (centered at > > the > > > > nitrogen) in the same plane. > > > > > > > > On Tue, Apr 4, 2017 at 10:38 AM, Phillip Rauscher < > > > pmrausc...@uchicago.edu > > > > > > > > > wrote: > > > > > > > > > Hello all, > > > > > > > > > > I've noticed that in some of the force fields (in the aminoacid.rtp > > > > > files), an improper dihedral is applied to the nitrogens in the > > peptide > > > > > bond (and sometimes other amine groups as well), which are all sp3 > > > > > hybridized with one lone pair. Interestingly, the dihedral > potential > > > > > parameters serve to keep the groups trigonal planar, rather than > > > > > tetrahedral. More specifically, I've seen this in OPLS, Amber03, > and > > > > > Charmm27 - enough to indicate that it's not a mistake (besides the > > fact > > > > > that it's applied to ALL amino acids!) The functional form of the > > > > improper > > > > > potential varies between force fields, but the lowest energy angle > is > > > > > always 0 or 180 indicating planar structure. > > > > > > > > > > Why is this done? I've done some digging through the GROMACS > > > > publications > > > > > as well as those for the force fields and can't seem to find any > > > > reference > > > > > to this practice? Is it an attempt to "average out" nitrogen > > > inversions? > > > > > Is it just to eliminate a chiral center? > > > > > > > > > > Thanks for your help! > > > > > > > > > > -Phil Rauscher > > > > > > > > > > -- > > > > > Phil Rauscher > > > > > Graduate Student > > > > > de Pablo and Rowan Research Groups > > > > > Institute for Molecular Engineering > > > > > University of Chicago > > > > > > > > > > > > > > > > > > > > > -- > > > > Phil Rauscher > > > > Graduate Student > > > > de Pablo and Rowan Research Groups > > > > Institute for Molecular Engineering > > > > University of Chicago > > > > -- > > > > 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. > > > > > > > > > > > -- > > Phil Rauscher > > Graduate Student > > de Pablo and Rowan Research Groups > > Institute for Molecular Engineering > > University of Chicago > > -- > > 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. > -- Phil Rauscher Graduate Student de Pablo and Rowan Research Groups Institute for Molecular Engineering University of Chicago -- 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.
