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.
