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? Thanks. Paolo -- 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.