Hi Justin, indeed there are only six bonds in the topology files! As you said the hydrogen nomenclature in .rtp file is wrong.
Thanks a lot! Paolo Il giorno gio 23 apr 2020 alle ore 12:55 Justin Lemkul <jalem...@vt.edu> ha scritto: > > > On 4/23/20 6:52 AM, Paolo Costa wrote: > > Dear Gromacs Users, > > > > I am trying to perform MD simulations of benzene molecule in a cube of > > water just for practicing. > > By following the tutorial > > https://www.svedruziclab.com/tutorials/gromacs/2-methane-in-water/, I > setup > > the residue Benzene within Amber99 force field. After the minimization > > however I got the C-H bonds of benzene distorted and unusually stretched. > > During the grompp procedure I got the following note: > > > > " In moleculetype 'Other' 6 atoms are not bound by a potential or > > constraint to any other atom in the same moleculetype. Although > > technically this might not cause issues in a simulation, this often > means > > that the user forgot to add a bond/potential/constraint or put > multiple > > molecules in the same moleculetype definition by mistake. Run with -v > to > > get information for each atom." > > > > Could it be related to the problem I am facing? > > > > Here the starting .pdb file of benzene: > > COMPND BENZENE > > REMARK 1 File created by GaussView 6.0.16 > > HETATM 1 C1 C6H6 0 0.968 1.903 0.000 > C > > HETATM 2 C2 C6H6 0 2.363 1.903 0.000 > C > > HETATM 3 C3 C6H6 0 3.060 3.111 0.000 > C > > HETATM 4 C4 C6H6 0 2.363 4.319 -0.001 > C > > HETATM 5 C5 C6H6 0 0.968 4.319 -0.002 > C > > HETATM 6 C6 C6H6 0 0.270 3.111 -0.001 > C > > HETATM 7 H1 C6H6 0 0.418 0.951 0.000 > H > > HETATM 8 H2 C6H6 0 2.912 0.951 0.001 > H > > HETATM 9 H3 C6H6 0 4.160 3.111 0.001 > H > > HETATM 10 H4 C6H6 0 2.913 5.272 -0.001 > H > > HETATM 11 H5 C6H6 0 0.418 5.272 -0.003 > H > > HETATM 12 H6 C6H6 0 -0.829 3.111 -0.001 > H > > END > > CONECT 1 2 6 7 > > CONECT 2 1 3 8 > > CONECT 3 2 4 9 > > CONECT 4 3 5 10 > > CONECT 5 4 6 11 > > CONECT 6 1 5 12 > > CONECT 7 1 > > CONECT 8 2 > > CONECT 9 3 > > CONECT 10 4 > > CONECT 11 5 > > CONECT 12 6 > > > > Here the .rtp file included in Amber99.ff: > > [ C6H6 ] > > [ atoms ] > > C1 CA -0.1285 1 > > C2 CA -0.1285 2 > > C3 CA -0.1285 3 > > C4 CA -0.1285 4 > > C5 CA -0.1285 5 > > C6 CA -0.1285 6 > > H1 HA 0.1285 7 > > H2 HA 0.1285 8 > > H3 HA 0.1285 9 > > H4 HA 0.1285 10 > > H5 HA 0.1285 11 > > H6 HA 0.1285 12 > > [ bonds ] > > C1 H7 > > C1 C2 > > C1 C6 > > C2 C8 > > C2 C1 > > C2 C3 > > C3 H9 > > C3 C2 > > C3 C4 > > C4 H10 > > C4 C3 > > C4 C5 > > C5 H11 > > C5 C4 > > C5 C6 > > C6 H12 > > C6 C5 > > C6 C1 > > > > Can somebody help me to figure out such issue? > > The bonds in the .rtp file are wrong. The hydrogen nomenclature is > incorrect so you do not have any C-H bonds in the topology. You can > verify this for yourself. You probably have 6 bonds instead of 12. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > 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. > -- Paolo Costa, Ph.D. Postdoctoral Researcher Department of Chemistry and Biomolecular Sciences University of Ottawa 10 Marie Curie, Ottawa, ON K1N 6N5, Canada Room number: DRO 326 (D'Iorio Hall) -- 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.
